Job ID = 5790632 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 49,032,178 reads read : 49,032,178 reads written : 49,032,178 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR4018121.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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:29:17 49032178 reads; of these: 49032178 (100.00%) were unpaired; of these: 1765779 (3.60%) aligned 0 times 35610095 (72.63%) aligned exactly 1 time 11656304 (23.77%) aligned >1 times 96.40% overall alignment rate Time searching: 00:29:21 Overall time: 00:29:21 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 20 files... [bam_rmdupse_core] 16115471 / 47266399 = 0.3409 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 05:01:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX2011879/SRX2011879.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX2011879/SRX2011879.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX2011879/SRX2011879.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX2011879/SRX2011879.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 05:01:26: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:01:26: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:01:33: 1000000 INFO @ Wed, 22 Apr 2020 05:01:40: 2000000 INFO @ Wed, 22 Apr 2020 05:01:46: 3000000 INFO @ Wed, 22 Apr 2020 05:01:53: 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 05:01:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX2011879/SRX2011879.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX2011879/SRX2011879.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX2011879/SRX2011879.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX2011879/SRX2011879.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 05:01:56: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:01:56: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:02:00: 5000000 INFO @ Wed, 22 Apr 2020 05:02:03: 1000000 INFO @ Wed, 22 Apr 2020 05:02:07: 6000000 INFO @ Wed, 22 Apr 2020 05:02:11: 2000000 INFO @ Wed, 22 Apr 2020 05:02:14: 7000000 INFO @ Wed, 22 Apr 2020 05:02:18: 3000000 INFO @ Wed, 22 Apr 2020 05:02:21: 8000000 INFO @ Wed, 22 Apr 2020 05:02:25: 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 05:02:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX2011879/SRX2011879.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX2011879/SRX2011879.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX2011879/SRX2011879.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX2011879/SRX2011879.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 05:02:26: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:02:26: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:02:28: 9000000 INFO @ Wed, 22 Apr 2020 05:02:32: 5000000 INFO @ Wed, 22 Apr 2020 05:02:34: 1000000 INFO @ Wed, 22 Apr 2020 05:02:35: 10000000 INFO @ Wed, 22 Apr 2020 05:02:39: 6000000 INFO @ Wed, 22 Apr 2020 05:02:41: 2000000 INFO @ Wed, 22 Apr 2020 05:02:43: 11000000 INFO @ Wed, 22 Apr 2020 05:02:47: 7000000 INFO @ Wed, 22 Apr 2020 05:02:48: 3000000 INFO @ Wed, 22 Apr 2020 05:02:50: 12000000 INFO @ Wed, 22 Apr 2020 05:02:54: 8000000 INFO @ Wed, 22 Apr 2020 05:02:56: 4000000 INFO @ Wed, 22 Apr 2020 05:02:57: 13000000 INFO @ Wed, 22 Apr 2020 05:03:01: 9000000 INFO @ Wed, 22 Apr 2020 05:03:03: 5000000 INFO @ Wed, 22 Apr 2020 05:03:04: 14000000 INFO @ Wed, 22 Apr 2020 05:03:09: 10000000 INFO @ Wed, 22 Apr 2020 05:03:10: 6000000 INFO @ Wed, 22 Apr 2020 05:03:11: 15000000 INFO @ Wed, 22 Apr 2020 05:03:16: 11000000 INFO @ Wed, 22 Apr 2020 05:03:18: 7000000 INFO @ Wed, 22 Apr 2020 05:03:18: 16000000 INFO @ Wed, 22 Apr 2020 05:03:23: 12000000 INFO @ Wed, 22 Apr 2020 05:03:25: 8000000 INFO @ Wed, 22 Apr 2020 05:03:25: 17000000 INFO @ Wed, 22 Apr 2020 05:03:30: 13000000 INFO @ Wed, 22 Apr 2020 05:03:32: 9000000 INFO @ Wed, 22 Apr 2020 05:03:32: 18000000 INFO @ Wed, 22 Apr 2020 05:03:38: 14000000 INFO @ Wed, 22 Apr 2020 05:03:39: 10000000 INFO @ Wed, 22 Apr 2020 05:03:40: 19000000 INFO @ Wed, 22 Apr 2020 05:03:45: 15000000 INFO @ Wed, 22 Apr 2020 05:03:46: 11000000 INFO @ Wed, 22 Apr 2020 05:03:47: 20000000 INFO @ Wed, 22 Apr 2020 05:03:52: 16000000 INFO @ Wed, 22 Apr 2020 05:03:54: 21000000 INFO @ Wed, 22 Apr 2020 05:03:54: 12000000 INFO @ Wed, 22 Apr 2020 05:03:59: 17000000 INFO @ Wed, 22 Apr 2020 05:04:01: 22000000 INFO @ Wed, 22 Apr 2020 05:04:01: 13000000 INFO @ Wed, 22 Apr 2020 05:04:07: 18000000 INFO @ Wed, 22 Apr 2020 05:04:08: 23000000 INFO @ Wed, 22 Apr 2020 05:04:08: 14000000 INFO @ Wed, 22 Apr 2020 05:04:14: 19000000 INFO @ Wed, 22 Apr 2020 05:04:15: 24000000 INFO @ Wed, 22 Apr 2020 05:04:15: 15000000 INFO @ Wed, 22 Apr 2020 05:04:21: 20000000 INFO @ Wed, 22 Apr 2020 05:04:22: 25000000 INFO @ Wed, 22 Apr 2020 05:04:23: 16000000 INFO @ Wed, 22 Apr 2020 05:04:28: 21000000 INFO @ Wed, 22 Apr 2020 05:04:29: 26000000 INFO @ Wed, 22 Apr 2020 05:04:30: 17000000 INFO @ Wed, 22 Apr 2020 05:04:35: 22000000 INFO @ Wed, 22 Apr 2020 05:04:36: 27000000 INFO @ Wed, 22 Apr 2020 05:04:37: 18000000 INFO @ Wed, 22 Apr 2020 05:04:43: 23000000 INFO @ Wed, 22 Apr 2020 05:04:43: 28000000 INFO @ Wed, 22 Apr 2020 05:04:44: 19000000 INFO @ Wed, 22 Apr 2020 05:04:50: 24000000 INFO @ Wed, 22 Apr 2020 05:04:50: 29000000 INFO @ Wed, 22 Apr 2020 05:04:52: 20000000 INFO @ Wed, 22 Apr 2020 05:04:57: 25000000 INFO @ Wed, 22 Apr 2020 05:04:58: 30000000 INFO @ Wed, 22 Apr 2020 05:04:59: 21000000 INFO @ Wed, 22 Apr 2020 05:05:04: 26000000 INFO @ Wed, 22 Apr 2020 05:05:05: 31000000 INFO @ Wed, 22 Apr 2020 05:05:06: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 05:05:06: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 05:05:06: #1 total tags in treatment: 31150928 INFO @ Wed, 22 Apr 2020 05:05:06: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:05:06: #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 05:05:06: 22000000 INFO @ Wed, 22 Apr 2020 05:05:06: #1 tags after filtering in treatment: 31150830 INFO @ Wed, 22 Apr 2020 05:05:06: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:05:06: #1 finished! INFO @ Wed, 22 Apr 2020 05:05:06: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:05:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:05:09: #2 number of paired peaks: 6180 INFO @ Wed, 22 Apr 2020 05:05:09: start model_add_line... INFO @ Wed, 22 Apr 2020 05:05:09: start X-correlation... INFO @ Wed, 22 Apr 2020 05:05:09: end of X-cor INFO @ Wed, 22 Apr 2020 05:05:09: #2 finished! INFO @ Wed, 22 Apr 2020 05:05:09: #2 predicted fragment length is 51 bps INFO @ Wed, 22 Apr 2020 05:05:09: #2 alternative fragment length(s) may be 51 bps INFO @ Wed, 22 Apr 2020 05:05:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX2011879/SRX2011879.05_model.r WARNING @ Wed, 22 Apr 2020 05:05:09: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 05:05:09: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Wed, 22 Apr 2020 05:05:09: #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 05:05:09: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:05:09: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:05:11: 27000000 INFO @ Wed, 22 Apr 2020 05:05:13: 23000000 INFO @ Wed, 22 Apr 2020 05:05:18: 28000000 INFO @ Wed, 22 Apr 2020 05:05:20: 24000000 INFO @ Wed, 22 Apr 2020 05:05:25: 29000000 INFO @ Wed, 22 Apr 2020 05:05:27: 25000000 INFO @ Wed, 22 Apr 2020 05:05:32: 30000000 INFO @ Wed, 22 Apr 2020 05:05:33: 26000000 INFO @ Wed, 22 Apr 2020 05:05:39: 31000000 INFO @ Wed, 22 Apr 2020 05:05:40: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 05:05:40: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 05:05:40: #1 total tags in treatment: 31150928 INFO @ Wed, 22 Apr 2020 05:05:40: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:05:40: #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 05:05:40: 27000000 INFO @ Wed, 22 Apr 2020 05:05:40: #1 tags after filtering in treatment: 31150830 INFO @ Wed, 22 Apr 2020 05:05:40: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:05:40: #1 finished! INFO @ Wed, 22 Apr 2020 05:05:40: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:05:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:05:43: #2 number of paired peaks: 6180 INFO @ Wed, 22 Apr 2020 05:05:43: start model_add_line... INFO @ Wed, 22 Apr 2020 05:05:43: start X-correlation... INFO @ Wed, 22 Apr 2020 05:05:43: end of X-cor INFO @ Wed, 22 Apr 2020 05:05:43: #2 finished! INFO @ Wed, 22 Apr 2020 05:05:43: #2 predicted fragment length is 51 bps INFO @ Wed, 22 Apr 2020 05:05:43: #2 alternative fragment length(s) may be 51 bps INFO @ Wed, 22 Apr 2020 05:05:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX2011879/SRX2011879.10_model.r WARNING @ Wed, 22 Apr 2020 05:05:43: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 05:05:43: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Wed, 22 Apr 2020 05:05:43: #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 05:05:43: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:05:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:05:47: 28000000 INFO @ Wed, 22 Apr 2020 05:05:53: 29000000 INFO @ Wed, 22 Apr 2020 05:06:00: 30000000 INFO @ Wed, 22 Apr 2020 05:06:06: 31000000 INFO @ Wed, 22 Apr 2020 05:06:08: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 05:06:08: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 05:06:08: #1 total tags in treatment: 31150928 INFO @ Wed, 22 Apr 2020 05:06:08: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:06:08: #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 05:06:08: #1 tags after filtering in treatment: 31150830 INFO @ Wed, 22 Apr 2020 05:06:08: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:06:08: #1 finished! INFO @ Wed, 22 Apr 2020 05:06:08: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:06:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:06:11: #2 number of paired peaks: 6180 INFO @ Wed, 22 Apr 2020 05:06:11: start model_add_line... INFO @ Wed, 22 Apr 2020 05:06:11: start X-correlation... INFO @ Wed, 22 Apr 2020 05:06:11: end of X-cor INFO @ Wed, 22 Apr 2020 05:06:11: #2 finished! INFO @ Wed, 22 Apr 2020 05:06:11: #2 predicted fragment length is 51 bps INFO @ Wed, 22 Apr 2020 05:06:11: #2 alternative fragment length(s) may be 51 bps INFO @ Wed, 22 Apr 2020 05:06:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX2011879/SRX2011879.20_model.r WARNING @ Wed, 22 Apr 2020 05:06:11: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 05:06:11: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Wed, 22 Apr 2020 05:06:11: #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 05:06:11: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:06:11: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:06:19: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:06:53: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:06:53: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX2011879/SRX2011879.05_peaks.xls INFO @ Wed, 22 Apr 2020 05:06:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX2011879/SRX2011879.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:06:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX2011879/SRX2011879.05_summits.bed INFO @ Wed, 22 Apr 2020 05:06:53: Done! pass1 - making usageList (53 chroms): 1 millis pass2 - checking and writing primary data (1921 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 05:07:19: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:07:28: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX2011879/SRX2011879.10_peaks.xls INFO @ Wed, 22 Apr 2020 05:07:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX2011879/SRX2011879.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:07:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX2011879/SRX2011879.10_summits.bed INFO @ Wed, 22 Apr 2020 05:07:28: Done! pass1 - making usageList (41 chroms): 1 millis pass2 - checking and writing primary data (1096 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 05:07:54: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX2011879/SRX2011879.20_peaks.xls INFO @ Wed, 22 Apr 2020 05:07:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX2011879/SRX2011879.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:07:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX2011879/SRX2011879.20_summits.bed INFO @ Wed, 22 Apr 2020 05:07:54: Done! pass1 - making usageList (33 chroms): 0 millis pass2 - checking and writing primary data (527 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。