Job ID = 5790703 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 41,047,740 reads read : 41,047,740 reads written : 41,047,740 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR8982436.sra.cache’: 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: 00:00:00 Multiseed full-index search: 00:12:41 41047740 reads; of these: 41047740 (100.00%) were unpaired; of these: 8513082 (20.74%) aligned 0 times 21497280 (52.37%) aligned exactly 1 time 11037378 (26.89%) aligned >1 times 79.26% overall alignment rate Time searching: 00:12:42 Overall time: 00:12:42 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 12 files... [bam_rmdupse_core] 5462858 / 32534658 = 0.1679 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 06:37:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761734/SRX5761734.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761734/SRX5761734.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761734/SRX5761734.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761734/SRX5761734.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 @ Wed, 22 Apr 2020 06:37:11: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:37:11: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:37:17: 1000000 INFO @ Wed, 22 Apr 2020 06:37:22: 2000000 INFO @ Wed, 22 Apr 2020 06:37:28: 3000000 INFO @ Wed, 22 Apr 2020 06:37:35: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 06:37:40: 5000000 INFO @ Wed, 22 Apr 2020 06:37:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761734/SRX5761734.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761734/SRX5761734.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761734/SRX5761734.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761734/SRX5761734.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 @ Wed, 22 Apr 2020 06:37:41: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:37:41: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:37:46: 6000000 INFO @ Wed, 22 Apr 2020 06:37:47: 1000000 INFO @ Wed, 22 Apr 2020 06:37:52: 7000000 INFO @ Wed, 22 Apr 2020 06:37:53: 2000000 INFO @ Wed, 22 Apr 2020 06:37:58: 8000000 INFO @ Wed, 22 Apr 2020 06:37:59: 3000000 INFO @ Wed, 22 Apr 2020 06:38:04: 9000000 INFO @ Wed, 22 Apr 2020 06:38:05: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 06:38:10: 10000000 INFO @ Wed, 22 Apr 2020 06:38:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761734/SRX5761734.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761734/SRX5761734.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761734/SRX5761734.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761734/SRX5761734.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 @ Wed, 22 Apr 2020 06:38:11: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:38:11: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:38:12: 5000000 INFO @ Wed, 22 Apr 2020 06:38:16: 11000000 INFO @ Wed, 22 Apr 2020 06:38:18: 1000000 INFO @ Wed, 22 Apr 2020 06:38:18: 6000000 INFO @ Wed, 22 Apr 2020 06:38:22: 12000000 INFO @ Wed, 22 Apr 2020 06:38:25: 2000000 INFO @ Wed, 22 Apr 2020 06:38:25: 7000000 INFO @ Wed, 22 Apr 2020 06:38:28: 13000000 INFO @ Wed, 22 Apr 2020 06:38:31: 3000000 INFO @ Wed, 22 Apr 2020 06:38:32: 8000000 INFO @ Wed, 22 Apr 2020 06:38:35: 14000000 INFO @ Wed, 22 Apr 2020 06:38:37: 4000000 INFO @ Wed, 22 Apr 2020 06:38:38: 9000000 INFO @ Wed, 22 Apr 2020 06:38:41: 15000000 INFO @ Wed, 22 Apr 2020 06:38:43: 5000000 INFO @ Wed, 22 Apr 2020 06:38:44: 10000000 INFO @ Wed, 22 Apr 2020 06:38:47: 16000000 INFO @ Wed, 22 Apr 2020 06:38:49: 6000000 INFO @ Wed, 22 Apr 2020 06:38:50: 11000000 INFO @ Wed, 22 Apr 2020 06:38:53: 17000000 INFO @ Wed, 22 Apr 2020 06:38:55: 7000000 INFO @ Wed, 22 Apr 2020 06:38:56: 12000000 INFO @ Wed, 22 Apr 2020 06:38:59: 18000000 INFO @ Wed, 22 Apr 2020 06:39:01: 8000000 INFO @ Wed, 22 Apr 2020 06:39:03: 13000000 INFO @ Wed, 22 Apr 2020 06:39:05: 19000000 INFO @ Wed, 22 Apr 2020 06:39:07: 9000000 INFO @ Wed, 22 Apr 2020 06:39:09: 14000000 INFO @ Wed, 22 Apr 2020 06:39:11: 20000000 INFO @ Wed, 22 Apr 2020 06:39:13: 10000000 INFO @ Wed, 22 Apr 2020 06:39:15: 15000000 INFO @ Wed, 22 Apr 2020 06:39:17: 21000000 INFO @ Wed, 22 Apr 2020 06:39:19: 11000000 INFO @ Wed, 22 Apr 2020 06:39:21: 16000000 INFO @ Wed, 22 Apr 2020 06:39:23: 22000000 INFO @ Wed, 22 Apr 2020 06:39:25: 12000000 INFO @ Wed, 22 Apr 2020 06:39:27: 17000000 INFO @ Wed, 22 Apr 2020 06:39:29: 23000000 INFO @ Wed, 22 Apr 2020 06:39:31: 13000000 INFO @ Wed, 22 Apr 2020 06:39:33: 18000000 INFO @ Wed, 22 Apr 2020 06:39:35: 24000000 INFO @ Wed, 22 Apr 2020 06:39:37: 14000000 INFO @ Wed, 22 Apr 2020 06:39:39: 19000000 INFO @ Wed, 22 Apr 2020 06:39:41: 25000000 INFO @ Wed, 22 Apr 2020 06:39:43: 15000000 INFO @ Wed, 22 Apr 2020 06:39:45: 20000000 INFO @ Wed, 22 Apr 2020 06:39:47: 26000000 INFO @ Wed, 22 Apr 2020 06:39:49: 16000000 INFO @ Wed, 22 Apr 2020 06:39:51: 21000000 INFO @ Wed, 22 Apr 2020 06:39:53: 27000000 INFO @ Wed, 22 Apr 2020 06:39:54: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:39:54: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:39:54: #1 total tags in treatment: 27071800 INFO @ Wed, 22 Apr 2020 06:39:54: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:39:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:39:54: #1 tags after filtering in treatment: 27071689 INFO @ Wed, 22 Apr 2020 06:39:54: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:39:54: #1 finished! INFO @ Wed, 22 Apr 2020 06:39:54: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:39:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:39:54: 17000000 INFO @ Wed, 22 Apr 2020 06:39:56: #2 number of paired peaks: 5476 INFO @ Wed, 22 Apr 2020 06:39:56: start model_add_line... INFO @ Wed, 22 Apr 2020 06:39:57: start X-correlation... INFO @ Wed, 22 Apr 2020 06:39:57: end of X-cor INFO @ Wed, 22 Apr 2020 06:39:57: #2 finished! INFO @ Wed, 22 Apr 2020 06:39:57: #2 predicted fragment length is 36 bps INFO @ Wed, 22 Apr 2020 06:39:57: #2 alternative fragment length(s) may be 36,181,219,398,579 bps INFO @ Wed, 22 Apr 2020 06:39:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761734/SRX5761734.05_model.r WARNING @ Wed, 22 Apr 2020 06:39:57: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 06:39:57: #2 You may need to consider one of the other alternative d(s): 36,181,219,398,579 WARNING @ Wed, 22 Apr 2020 06:39:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 06:39:57: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:39:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:39:57: 22000000 INFO @ Wed, 22 Apr 2020 06:40:00: 18000000 INFO @ Wed, 22 Apr 2020 06:40:03: 23000000 INFO @ Wed, 22 Apr 2020 06:40:06: 19000000 INFO @ Wed, 22 Apr 2020 06:40:10: 24000000 INFO @ Wed, 22 Apr 2020 06:40:12: 20000000 INFO @ Wed, 22 Apr 2020 06:40:16: 25000000 INFO @ Wed, 22 Apr 2020 06:40:17: 21000000 INFO @ Wed, 22 Apr 2020 06:40:22: 26000000 INFO @ Wed, 22 Apr 2020 06:40:23: 22000000 INFO @ Wed, 22 Apr 2020 06:40:28: 27000000 INFO @ Wed, 22 Apr 2020 06:40:29: 23000000 INFO @ Wed, 22 Apr 2020 06:40:29: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:40:29: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:40:29: #1 total tags in treatment: 27071800 INFO @ Wed, 22 Apr 2020 06:40:29: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:40:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:40:29: #1 tags after filtering in treatment: 27071689 INFO @ Wed, 22 Apr 2020 06:40:29: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:40:29: #1 finished! INFO @ Wed, 22 Apr 2020 06:40:29: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:40:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:40:32: #2 number of paired peaks: 5476 INFO @ Wed, 22 Apr 2020 06:40:32: start model_add_line... INFO @ Wed, 22 Apr 2020 06:40:32: start X-correlation... INFO @ Wed, 22 Apr 2020 06:40:32: end of X-cor INFO @ Wed, 22 Apr 2020 06:40:32: #2 finished! INFO @ Wed, 22 Apr 2020 06:40:32: #2 predicted fragment length is 36 bps INFO @ Wed, 22 Apr 2020 06:40:32: #2 alternative fragment length(s) may be 36,181,219,398,579 bps INFO @ Wed, 22 Apr 2020 06:40:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761734/SRX5761734.10_model.r WARNING @ Wed, 22 Apr 2020 06:40:32: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 06:40:32: #2 You may need to consider one of the other alternative d(s): 36,181,219,398,579 WARNING @ Wed, 22 Apr 2020 06:40:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 06:40:32: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:40:32: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:40:34: 24000000 INFO @ Wed, 22 Apr 2020 06:40:40: 25000000 INFO @ Wed, 22 Apr 2020 06:40:45: 26000000 INFO @ Wed, 22 Apr 2020 06:40:50: 27000000 INFO @ Wed, 22 Apr 2020 06:40:51: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:40:51: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:40:51: #1 total tags in treatment: 27071800 INFO @ Wed, 22 Apr 2020 06:40:51: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:40:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:40:52: #1 tags after filtering in treatment: 27071689 INFO @ Wed, 22 Apr 2020 06:40:52: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:40:52: #1 finished! INFO @ Wed, 22 Apr 2020 06:40:52: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:40:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:40:54: #2 number of paired peaks: 5476 INFO @ Wed, 22 Apr 2020 06:40:54: start model_add_line... INFO @ Wed, 22 Apr 2020 06:40:54: start X-correlation... INFO @ Wed, 22 Apr 2020 06:40:54: end of X-cor INFO @ Wed, 22 Apr 2020 06:40:54: #2 finished! INFO @ Wed, 22 Apr 2020 06:40:54: #2 predicted fragment length is 36 bps INFO @ Wed, 22 Apr 2020 06:40:54: #2 alternative fragment length(s) may be 36,181,219,398,579 bps INFO @ Wed, 22 Apr 2020 06:40:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761734/SRX5761734.20_model.r WARNING @ Wed, 22 Apr 2020 06:40:54: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 06:40:54: #2 You may need to consider one of the other alternative d(s): 36,181,219,398,579 WARNING @ Wed, 22 Apr 2020 06:40:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 06:40:54: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:40:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:40:57: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:41:27: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761734/SRX5761734.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:41:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761734/SRX5761734.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:41:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761734/SRX5761734.05_summits.bed INFO @ Wed, 22 Apr 2020 06:41:27: Done! pass1 - making usageList (58 chroms): 1 millis pass2 - checking and writing primary data (2338 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:41:30: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:41:54: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:42:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761734/SRX5761734.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:42:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761734/SRX5761734.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:42:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761734/SRX5761734.10_summits.bed INFO @ Wed, 22 Apr 2020 06:42:01: Done! pass1 - making usageList (47 chroms): 0 millis pass2 - checking and writing primary data (1364 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:42:24: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761734/SRX5761734.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:42:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761734/SRX5761734.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:42:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761734/SRX5761734.20_summits.bed INFO @ Wed, 22 Apr 2020 06:42:24: Done! pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (630 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。