Job ID = 2001524 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T19:10:38 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 22,931,014 reads read : 22,931,014 reads written : 22,931,014 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:06:40 22931014 reads; of these: 22931014 (100.00%) were unpaired; of these: 435672 (1.90%) aligned 0 times 20147227 (87.86%) aligned exactly 1 time 2348115 (10.24%) aligned >1 times 98.10% overall alignment rate Time searching: 00:06:42 Overall time: 00:06:42 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 10880938 / 22495342 = 0.4837 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 05 Jul 2019 04:32:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101869/ERX101869.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101869/ERX101869.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101869/ERX101869.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101869/ERX101869.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 04:32:05: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:32:05: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:32:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101869/ERX101869.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101869/ERX101869.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101869/ERX101869.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101869/ERX101869.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 04:32:06: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:32:06: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:32:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101869/ERX101869.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101869/ERX101869.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101869/ERX101869.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101869/ERX101869.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 04:32:08: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:32:08: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:32:15: 1000000 INFO @ Fri, 05 Jul 2019 04:32:16: 1000000 INFO @ Fri, 05 Jul 2019 04:32:19: 1000000 INFO @ Fri, 05 Jul 2019 04:32:23: 2000000 INFO @ Fri, 05 Jul 2019 04:32:26: 2000000 INFO @ Fri, 05 Jul 2019 04:32:30: 2000000 INFO @ Fri, 05 Jul 2019 04:32:30: 3000000 INFO @ Fri, 05 Jul 2019 04:32:36: 3000000 INFO @ Fri, 05 Jul 2019 04:32:38: 4000000 INFO @ Fri, 05 Jul 2019 04:32:42: 3000000 INFO @ Fri, 05 Jul 2019 04:32:46: 5000000 INFO @ Fri, 05 Jul 2019 04:32:46: 4000000 INFO @ Fri, 05 Jul 2019 04:32:53: 4000000 INFO @ Fri, 05 Jul 2019 04:32:55: 6000000 INFO @ Fri, 05 Jul 2019 04:32:56: 5000000 INFO @ Fri, 05 Jul 2019 04:33:03: 5000000 INFO @ Fri, 05 Jul 2019 04:33:05: 7000000 INFO @ Fri, 05 Jul 2019 04:33:06: 6000000 INFO @ Fri, 05 Jul 2019 04:33:14: 6000000 INFO @ Fri, 05 Jul 2019 04:33:15: 8000000 INFO @ Fri, 05 Jul 2019 04:33:17: 7000000 INFO @ Fri, 05 Jul 2019 04:33:25: 7000000 INFO @ Fri, 05 Jul 2019 04:33:26: 9000000 INFO @ Fri, 05 Jul 2019 04:33:26: 8000000 INFO @ Fri, 05 Jul 2019 04:33:35: 8000000 INFO @ Fri, 05 Jul 2019 04:33:36: 9000000 INFO @ Fri, 05 Jul 2019 04:33:37: 10000000 INFO @ Fri, 05 Jul 2019 04:33:46: 10000000 INFO @ Fri, 05 Jul 2019 04:33:46: 9000000 INFO @ Fri, 05 Jul 2019 04:33:47: 11000000 INFO @ Fri, 05 Jul 2019 04:33:53: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:33:53: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:33:53: #1 total tags in treatment: 11614404 INFO @ Fri, 05 Jul 2019 04:33:53: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:33:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 04:33:54: #1 tags after filtering in treatment: 11614135 INFO @ Fri, 05 Jul 2019 04:33:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:33:54: #1 finished! INFO @ Fri, 05 Jul 2019 04:33:54: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:33:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:33:57: 11000000 INFO @ Fri, 05 Jul 2019 04:33:57: 10000000 INFO @ Fri, 05 Jul 2019 04:33:58: #2 number of paired peaks: 52246 INFO @ Fri, 05 Jul 2019 04:33:58: start model_add_line... INFO @ Fri, 05 Jul 2019 04:33:58: start X-correlation... INFO @ Fri, 05 Jul 2019 04:33:58: end of X-cor INFO @ Fri, 05 Jul 2019 04:33:58: #2 finished! INFO @ Fri, 05 Jul 2019 04:33:58: #2 predicted fragment length is 138 bps INFO @ Fri, 05 Jul 2019 04:33:58: #2 alternative fragment length(s) may be 4,138 bps INFO @ Fri, 05 Jul 2019 04:33:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101869/ERX101869.10_model.r INFO @ Fri, 05 Jul 2019 04:33:58: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:33:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:34:02: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:34:02: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:34:02: #1 total tags in treatment: 11614404 INFO @ Fri, 05 Jul 2019 04:34:02: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:34:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 04:34:03: #1 tags after filtering in treatment: 11614135 INFO @ Fri, 05 Jul 2019 04:34:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:34:03: #1 finished! INFO @ Fri, 05 Jul 2019 04:34:03: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:34:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:34:06: #2 number of paired peaks: 52246 INFO @ Fri, 05 Jul 2019 04:34:06: start model_add_line... INFO @ Fri, 05 Jul 2019 04:34:07: start X-correlation... INFO @ Fri, 05 Jul 2019 04:34:07: end of X-cor INFO @ Fri, 05 Jul 2019 04:34:07: #2 finished! INFO @ Fri, 05 Jul 2019 04:34:07: #2 predicted fragment length is 138 bps INFO @ Fri, 05 Jul 2019 04:34:07: #2 alternative fragment length(s) may be 4,138 bps INFO @ Fri, 05 Jul 2019 04:34:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101869/ERX101869.05_model.r INFO @ Fri, 05 Jul 2019 04:34:07: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:34:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:34:07: 11000000 INFO @ Fri, 05 Jul 2019 04:34:13: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:34:13: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:34:13: #1 total tags in treatment: 11614404 INFO @ Fri, 05 Jul 2019 04:34:13: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:34:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 04:34:14: #1 tags after filtering in treatment: 11614135 INFO @ Fri, 05 Jul 2019 04:34:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:34:14: #1 finished! INFO @ Fri, 05 Jul 2019 04:34:14: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:34:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:34:17: #2 number of paired peaks: 52246 INFO @ Fri, 05 Jul 2019 04:34:17: start model_add_line... INFO @ Fri, 05 Jul 2019 04:34:18: start X-correlation... INFO @ Fri, 05 Jul 2019 04:34:18: end of X-cor INFO @ Fri, 05 Jul 2019 04:34:18: #2 finished! INFO @ Fri, 05 Jul 2019 04:34:18: #2 predicted fragment length is 138 bps INFO @ Fri, 05 Jul 2019 04:34:18: #2 alternative fragment length(s) may be 4,138 bps INFO @ Fri, 05 Jul 2019 04:34:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101869/ERX101869.20_model.r INFO @ Fri, 05 Jul 2019 04:34:18: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:34:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:34:39: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:34:48: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:34:56: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:35:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101869/ERX101869.10_peaks.xls INFO @ Fri, 05 Jul 2019 04:35:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101869/ERX101869.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:35:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101869/ERX101869.10_summits.bed INFO @ Fri, 05 Jul 2019 04:35:02: Done! pass1 - making usageList (109 chroms): 10 millis pass2 - checking and writing primary data (32370 records, 4 fields): 53 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:35:10: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101869/ERX101869.05_peaks.xls INFO @ Fri, 05 Jul 2019 04:35:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101869/ERX101869.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:35:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101869/ERX101869.05_summits.bed INFO @ Fri, 05 Jul 2019 04:35:11: Done! pass1 - making usageList (128 chroms): 9 millis pass2 - checking and writing primary data (42457 records, 4 fields): 59 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:35:15: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101869/ERX101869.20_peaks.xls INFO @ Fri, 05 Jul 2019 04:35:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101869/ERX101869.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:35:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101869/ERX101869.20_summits.bed INFO @ Fri, 05 Jul 2019 04:35:16: Done! pass1 - making usageList (75 chroms): 5 millis pass2 - checking and writing primary data (19115 records, 4 fields): 27 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。