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Old 01-01-2016, 10:19 AM   #1
Mike_Brown
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Default fail to determine the sequence name

I am new to BAM file and samtools. I want to extract part of bam file by

Code:
samtools view _SRA_RUN_AUTO_ARCHIVE_TEST_vault_EGAR00001003032_5499_1.bam "Chr5:18000-45500" > output.bam

But I got

Code:
[bam_parse_region] fail to determine the sequence name.
[main_samview] region "Chr5:18000-45500" specifies an unknown reference name. Continue anyway.

What happened?
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Old 01-01-2016, 11:45 AM   #2
GenoMax
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Look at the header of the bam (samtools view -H) to make sure that your region specification matches the name of the chromosome in the header. It may just be a matter of using chr5 instead of Chr5.
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Old 01-01-2016, 12:28 PM   #3
lindenb
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cross posted: https://www.biostars.org/p/171195/
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Old 01-01-2016, 01:31 PM   #4
Mike_Brown
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Quote:
Originally Posted by GenoMax View Post
Look at the header of the bam (samtools view -H) to make sure that your region specification matches the name of the chromosome in the header. It may just be a matter of using chr5 instead of Chr5.
I already sorted the bam file, which is EGAR00001003032_5499_1.sort.bam

I also tried your method. But I did not find any "chr".
Code:
@HD	VN:1.0	SO:coordinate
@SQ	SN:1	LN:249250621	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:1b22b98cdeb4a9304cb5d48026a85128	SP:Human
@SQ	SN:2	LN:243199373	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:a0d9851da00400dec1098a9255ac712e	SP:Human
@SQ	SN:3	LN:198022430	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:fdfd811849cc2fadebc929bb925902e5	SP:Human
@SQ	SN:4	LN:191154276	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:23dccd106897542ad87d2765d28a19a1	SP:Human
@SQ	SN:5	LN:180915260	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:0740173db9ffd264d728f32784845cd7	SP:Human
@SQ	SN:6	LN:171115067	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:1d3a93a248d92a729ee764823acbbc6b	SP:Human
@SQ	SN:7	LN:159138663	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:618366e953d6aaad97dbe4777c29375e	SP:Human
@SQ	SN:8	LN:146364022	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:96f514a9929e410c6651697bded59aec	SP:Human
@SQ	SN:9	LN:141213431	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:3e273117f15e0a400f01055d9f393768	SP:Human
@SQ	SN:10	LN:135534747	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:988c28e000e84c26d552359af1ea2e1d	SP:Human
@SQ	SN:11	LN:135006516	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:98c59049a2df285c76ffb1c6db8f8b96	SP:Human
@SQ	SN:12	LN:133851895	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:51851ac0e1a115847ad36449b0015864	SP:Human
@SQ	SN:13	LN:115169878	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:283f8d7892baa81b510a015719ca7b0b	SP:Human
@SQ	SN:14	LN:107349540	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:98f3cae32b2a2e9524bc19813927542e	SP:Human
@SQ	SN:15	LN:102531392	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:e5645a794a8238215b2cd77acb95a078	SP:Human
@SQ	SN:16	LN:90354753	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:fc9b1a7b42b97a864f56b348b06095e6	SP:Human
@SQ	SN:17	LN:81195210	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:351f64d4f4f9ddd45b35336ad97aa6de	SP:Human
@SQ	SN:18	LN:78077248	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c	SP:Human
@SQ	SN:19	LN:59128983	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:1aacd71f30db8e561810913e0b72636d	SP:Human
@SQ	SN:20	LN:63025520	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:0dec9660ec1efaaf33281c0d5ea2560f	SP:Human
@SQ	SN:21	LN:48129895	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:2979a6085bfe28e3ad6f552f361ed74d	SP:Human
@SQ	SN:22	LN:51304566	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:a718acaa6135fdca8357d5bfe94211dd	SP:Human
@SQ	SN:X	LN:155270560	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:7e0e2e580297b7764e31dbc80c2540dd	SP:Human
@SQ	SN:Y	LN:59373566	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:1fa3474750af0948bdf97d5a0ee52e51	SP:Human
@SQ	SN:MT	LN:16569	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:c68f52674c9fb33aef52dcf399755519	SP:Human
@SQ	SN:GL000207.1	LN:4262	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:f3814841f1939d3ca19072d9e89f3fd7	SP:Human
@SQ	SN:GL000226.1	LN:15008	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:1c1b2cd1fccbc0a99b6a447fa24d1504	SP:Human
@SQ	SN:GL000229.1	LN:19913	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:d0f40ec87de311d8e715b52e4c7062e1	SP:Human
@SQ	SN:GL000231.1	LN:27386	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:ba8882ce3a1efa2080e5d29b956568a4	SP:Human
@SQ	SN:GL000210.1	LN:27682	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:851106a74238044126131ce2a8e5847c	SP:Human
@SQ	SN:GL000239.1	LN:33824	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:99795f15702caec4fa1c4e15f8a29c07	SP:Human
@SQ	SN:GL000235.1	LN:34474	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:118a25ca210cfbcdfb6c2ebb249f9680	SP:Human
@SQ	SN:GL000201.1	LN:36148	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:dfb7e7ec60ffdcb85cb359ea28454ee9	SP:Human
@SQ	SN:GL000247.1	LN:36422	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:7de00226bb7df1c57276ca6baabafd15	SP:Human
@SQ	SN:GL000245.1	LN:36651	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:89bc61960f37d94abf0df2d481ada0ec	SP:Human
@SQ	SN:GL000197.1	LN:37175	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:6f5efdd36643a9b8c8ccad6f2f1edc7b	SP:Human
@SQ	SN:GL000203.1	LN:37498	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:96358c325fe0e70bee73436e8bb14dbd	SP:Human
@SQ	SN:GL000246.1	LN:38154	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:e4afcd31912af9d9c2546acf1cb23af2	SP:Human
@SQ	SN:GL000249.1	LN:38502	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:1d78abec37c15fe29a275eb08d5af236	SP:Human
@SQ	SN:GL000196.1	LN:38914	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:d92206d1bb4c3b4019c43c0875c06dc0	SP:Human
@SQ	SN:GL000248.1	LN:39786	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:5a8e43bec9be36c7b49c84d585107776	SP:Human
@SQ	SN:GL000244.1	LN:39929	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:0996b4475f353ca98bacb756ac479140	SP:Human
@SQ	SN:GL000238.1	LN:39939	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:131b1efc3270cc838686b54e7c34b17b	SP:Human
@SQ	SN:GL000202.1	LN:40103	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:06cbf126247d89664a4faebad130fe9c	SP:Human
@SQ	SN:GL000234.1	LN:40531	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:93f998536b61a56fd0ff47322a911d4b	SP:Human
@SQ	SN:GL000232.1	LN:40652	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:3e06b6741061ad93a8587531307057d8	SP:Human
@SQ	SN:GL000206.1	LN:41001	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:43f69e423533e948bfae5ce1d45bd3f1	SP:Human
@SQ	SN:GL000240.1	LN:41933	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:445a86173da9f237d7bcf41c6cb8cc62	SP:Human
@SQ	SN:GL000236.1	LN:41934	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:fdcd739913efa1fdc64b6c0cd7016779	SP:Human
@SQ	SN:GL000241.1	LN:42152	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:ef4258cdc5a45c206cea8fc3e1d858cf	SP:Human
@SQ	SN:GL000243.1	LN:43341	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:cc34279a7e353136741c9fce79bc4396	SP:Human
@SQ	SN:GL000242.1	LN:43523	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:2f8694fc47576bc81b5fe9e7de0ba49e	SP:Human
@SQ	SN:GL000230.1	LN:43691	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:b4eb71ee878d3706246b7c1dbef69299	SP:Human
@SQ	SN:GL000237.1	LN:45867	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:e0c82e7751df73f4f6d0ed30cdc853c0	SP:Human
@SQ	SN:GL000233.1	LN:45941	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:7fed60298a8d62ff808b74b6ce820001	SP:Human
@SQ	SN:GL000204.1	LN:81310	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:efc49c871536fa8d79cb0a06fa739722	SP:Human
@SQ	SN:GL000198.1	LN:90085	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:868e7784040da90d900d2d1b667a1383	SP:Human
@SQ	SN:GL000208.1	LN:92689	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:aa81be49bf3fe63a79bdc6a6f279abf6	SP:Human
@SQ	SN:GL000191.1	LN:106433	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:d75b436f50a8214ee9c2a51d30b2c2cc	SP:Human
@SQ	SN:GL000227.1	LN:128374	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:a4aead23f8053f2655e468bcc6ecdceb	SP:Human
@SQ	SN:GL000228.1	LN:129120	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:c5a17c97e2c1a0b6a9cc5a6b064b714f	SP:Human
@SQ	SN:GL000214.1	LN:137718	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:46c2032c37f2ed899eb41c0473319a69	SP:Human
@SQ	SN:GL000221.1	LN:155397	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:3238fb74ea87ae857f9c7508d315babb	SP:Human
@SQ	SN:GL000209.1	LN:159169	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:f40598e2a5a6b26e84a3775e0d1e2c81	SP:Human
@SQ	SN:GL000218.1	LN:161147	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:1d708b54644c26c7e01c2dad5426d38c	SP:Human
@SQ	SN:GL000220.1	LN:161802	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:fc35de963c57bf7648429e6454f1c9db	SP:Human
@SQ	SN:GL000213.1	LN:164239	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:9d424fdcc98866650b58f004080a992a	SP:Human
@SQ	SN:GL000211.1	LN:166566	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:7daaa45c66b288847b9b32b964e623d3	SP:Human
@SQ	SN:GL000199.1	LN:169874	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:569af3b73522fab4b40995ae4944e78e	SP:Human
@SQ	SN:GL000217.1	LN:172149	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:6d243e18dea1945fb7f2517615b8f52e	SP:Human
@SQ	SN:GL000216.1	LN:172294	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:642a232d91c486ac339263820aef7fe0	SP:Human
@SQ	SN:GL000215.1	LN:172545	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:5eb3b418480ae67a997957c909375a73	SP:Human
@SQ	SN:GL000205.1	LN:174588	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:d22441398d99caf673e9afb9a1908ec5	SP:Human
@SQ	SN:GL000219.1	LN:179198	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:f977edd13bac459cb2ed4a5457dba1b3	SP:Human
@SQ	SN:GL000224.1	LN:179693	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:d5b2fc04f6b41b212a4198a07f450e20	SP:Human
@SQ	SN:GL000223.1	LN:180455	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:399dfa03bf32022ab52a846f7ca35b30	SP:Human
@SQ	SN:GL000195.1	LN:182896	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:5d9ec007868d517e73543b005ba48535	SP:Human
@SQ	SN:GL000212.1	LN:186858	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:563531689f3dbd691331fd6c5730a88b	SP:Human
@SQ	SN:GL000222.1	LN:186861	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:6fe9abac455169f50470f5a6b01d0f59	SP:Human
@SQ	SN:GL000200.1	LN:187035	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:75e4c8d17cd4addf3917d1703cacaf25	SP:Human
@SQ	SN:GL000193.1	LN:189789	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:dbb6e8ece0b5de29da56601613007c2a	SP:Human
@SQ	SN:GL000194.1	LN:191469	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:6ac8f815bf8e845bb3031b73f812c012	SP:Human
@SQ	SN:GL000225.1	LN:211173	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:63945c3e6962f28ffd469719a747e73c	SP:Human
@SQ	SN:GL000192.1	LN:547496	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz	AS:NCBI37	M5:325ba9e808f669dfeee210fdd7b470ac	SP:Human
@RG	ID:1	PL:ILLUMINA	PU:101112_HS7_05499_A_80AGPABXX_1	LB:161494_H1 1350960	PI:339	DS:UK10K COHORT TWINSUK	DT:2010-11-12T00:00:00+0000	SM:UK10K_TW1537991	CN:SC
@PG	ID:SCS	PN:RTA	VN:1.7.48.0
@PG	ID:basecalling	PN:RTA	PP:SCS	VN:1.7.48.0
@PG	ID:bcl_to_qseq	PN:setupBclToQseq.py	PP:basecalling	VN:OLB-1.8.1a2 (OLB)
@PG	ID:fastq_creator	PN:qseq2fastq.pl	PP:bcl_to_qseq	CL:/software/solexa/bin/qseq2fastq.pl --md5 <md5_name> --fastqcheck <fastqcheck_name> --filter --unique <qseq_files> > <fastq_name>
@PG	ID:bwa_aln	PN:bwa aln	PP:fastq_creator	VN:0.5.8c (r1536)	CL:/software/solexa/bin/aligners/bwa/bwa-0.5.8c/bwa aln -q 15 -t 2 /nfs/repository/d0031/references/Homo_sapiens/GRCh37_53/all/bwa/Homo_sapiens.GRCh37.dna.all.fa /nfs/sf24/ILorHSany_sf24/analysis/101112_HS7_05499_A_80AGPABXX/Data/Intensities/PB_basecalls_20101122-091145/no_cal/archive/5499_1_1.fastq > /tmp/4iYp_FbYy2/1.sai;/software/solexa/bin/aligners/bwa/bwa-0.5.8c/bwa aln -q 15 -t 2 /nfs/repository/d0031/references/Homo_sapiens/GRCh37_53/all/bwa/Homo_sapiens.GRCh37.dna.all.fa /nfs/sf24/ILorHSany_sf24/analysis/101112_HS7_05499_A_80AGPABXX/Data/Intensities/PB_basecalls_20101122-091145/no_cal/archive/5499_1_2.fastq > /tmp/4iYp_FbYy2/2.sai;
@PG	ID:bwa_sam	PN:bwa sam	PP:bwa_aln	VN:0.5.8c (r1536)	CL:/software/solexa/bin/aligners/bwa/bwa-0.5.8c/bwa sampe /nfs/repository/d0031/references/Homo_sapiens/GRCh37_53/all/bwa/Homo_sapiens.GRCh37.dna.all.fa /tmp/4iYp_FbYy2/1.sai /tmp/4iYp_FbYy2/2.sai /nfs/sf24/ILorHSany_sf24/analysis/101112_HS7_05499_A_80AGPABXX/Data/Intensities/PB_basecalls_20101122-091145/no_cal/archive/5499_1_1.fastq /nfs/sf24/ILorHSany_sf24/analysis/101112_HS7_05499_A_80AGPABXX/Data/Intensities/PB_basecalls_20101122-091145/no_cal/archive/5499_1_2.fastq
@PG	ID:sam_header	PN:sam_header	PP:bwa_sam	VN:11872
@PG	ID:picard_samformatconverter	PN:Picard SamFormatConverter	PP:sam_header	VN:1.34	CL:/software/bin/java -jar /software/solexa/bin/aligners/picard/picard-tools-1.34/SamFormatConverter.jar VALIDATION_STRINGENCY=SILENT INPUT=/dev/stdin OUTPUT=/nfs/sf24/ILorHSany_sf24/analysis/101112_HS7_05499_A_80AGPABXX/Data/Intensities/PB_basecalls_20101122-091145/no_cal/archive/5499_1_unsorted.bam
@PG	ID:samtools_sort	PN:samtools	PP:picard_samformatconverter	VN:0.1.11 (r851)	CL:/software/solexa/bin/aligners/samtools/samtools-0.1.11/samtools sort
@PG	ID:picard_markduplicates	PN:Picard MarkDuplicates	PP:samtools_sort	VN:1.34	CL:/software/bin/java -Xmx3000m -jar /software/solexa/bin/aligners/picard/picard-tools-1.34/MarkDuplicates.jar INPUT= OUTPUT= METRICS_FILE= TMP_DIR= VALIDATION_STRINGENCY='SILENT' MAX_FILE_HANDLES_FOR_READ_ENDS_MAP='900' REMOVE_DUPLICATES='false' ASSUME_SORTED='true' VERBOSITY='ERROR' READ_NAME_REGEX='[a-zA-Z0-9_]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' CREATE_MD5_FILE='TRUE'
@PG	ID:sort_sam	PN:samtools	PP:picard_markduplicates	VN:0.1.12a (r862)	CL:/software/solexa/bin/aligners/samtools/samtools-0.1.12a/samtools sort -n - -o /nfs/sf45/uk10k_bam/5499/p8JUJAOMPb/56_qsgg7hz
@PG	ID:samtools_view	PN:samtools	PP:sort_sam	VN:0.1.12a (r862)	CL:/software/solexa/bin/aligners/samtools/samtools-0.1.12a/samtools view -o - -h -
@PG	ID:bwa_aln_read1	PN:bwa	PP:samtools_view	VN:0.5.8c (r1536)	CL:/software/solexa/bin/aligners/bwa/bwa-0.5.8c/bwa aln -q 15 -t 2 /nfs/repository/d0031/references/Homo_sapiens/1000Genomes/all/bwa/human_g1k_v37.fasta /nfs/sf45/uk10k_bam/5499/p8JUJAOMPb/read_1.fastq > /tmp/VsPazukTM7/read_1.sai
@PG	ID:bwa_aln_read2	PN:bwa	PP:bwa_aln_read1	VN:0.5.8c (r1536)	CL:/software/solexa/bin/aligners/bwa/bwa-0.5.8c/bwa aln -q 15 -t 2 /nfs/repository/d0031/references/Homo_sapiens/1000Genomes/all/bwa/human_g1k_v37.fasta /nfs/sf45/uk10k_bam/5499/p8JUJAOMPb/read_2.fastq > /tmp/VsPazukTM7/read_2.sai
@PG	ID:bwa_sampe	PN:bwa	PP:bwa_aln_read2	VN:0.5.8c (r1536)	CL:/software/solexa/bin/aligners/bwa/bwa-0.5.8c/bwa sampe /nfs/repository/d0031/references/Homo_sapiens/1000Genomes/all/bwa/human_g1k_v37.fasta /tmp/VsPazukTM7/read_1.sai /tmp/VsPazukTM7/read_2.sai /nfs/sf45/uk10k_bam/5499/p8JUJAOMPb/read_1.fastq /nfs/sf45/uk10k_bam/5499/p8JUJAOMPb/read_2.fastq
@PG	ID:samtools_view_2	PN:samtools	PP:bwa_sampe	VN:0.1.12a (r862)	CL:/software/solexa/bin/aligners/samtools/samtools-0.1.12a/samtools view -bhS -
@PG	ID:sort_sam_2	PN:samtools	PP:samtools_view_2	VN:0.1.12a (r862)	CL:/software/solexa/bin/aligners/samtools/samtools-0.1.12a/samtools sort - /nfs/sf45/uk10k_bam/5499/p8JUJAOMPb/duplicates_unmarked
@PG	ID:picard_markduplicates_2	PN:Picard MarkDuplicates	PP:sort_sam_2	VN:picard-tools-1.39	CL:/software/bin/java -jar /software/solexa/bin/aligners/picard/picard-tools-1.39/MarkDuplicates.jar INPUT=/nfs/sf45/uk10k_bam/5499/p8JUJAOMPb/duplicates_unmarked.bam OUTPUT=/nfs/sf45/uk10k_bam/5499/5499_1.bam METRICS_FILE=/nfs/sf45/uk10k_bam/5499/5499_1.bam.metrics VALIDATION_STRINGENCY='SILENT' MAX_FILE_HANDLES_FOR_READ_ENDS_MAP='900' REMOVE_DUPLICATES='false' ASSUME_SORTED='TRUE' VERBOSITY='ERROR' READ_NAME_REGEX='[a-zA-Z0-9_]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' CREATE_MD5_FILE='TRUE' CREATE_INDEX='TRUE'
@CO	npg_common::bam_align (v. 12752) used to realign from BAM
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Old 01-01-2016, 01:42 PM   #5
mastal
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Location: uk

Join Date: Mar 2009
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Looks like in your case the chromosomes are just named '1', '2', '3', etc, rather than chr1, chr2,

so you need to write '5:18000-45500" instead of "Chr5:18000-45500".
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