Job ID = 5720149 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,078,976 reads read : 34,157,952 reads written : 17,078,976 reads 0-length : 17,078,976 spots read : 56,326,135 reads read : 112,652,270 reads written : 56,326,135 reads 0-length : 56,326,135 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:17:34 73405111 reads; of these: 73405111 (100.00%) were unpaired; of these: 29863989 (40.68%) aligned 0 times 31880276 (43.43%) aligned exactly 1 time 11660846 (15.89%) aligned >1 times 59.32% overall alignment rate Time searching: 00:17:34 Overall time: 00:17:34 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 15868244 / 43541122 = 0.3644 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, 15 Apr 2020 22:11:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5702592/SRX5702592.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5702592/SRX5702592.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5702592/SRX5702592.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5702592/SRX5702592.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 15 Apr 2020 22:11:04: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:11:04: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:11:09: 1000000 INFO @ Wed, 15 Apr 2020 22:11:15: 2000000 INFO @ Wed, 15 Apr 2020 22:11:20: 3000000 INFO @ Wed, 15 Apr 2020 22:11:26: 4000000 INFO @ Wed, 15 Apr 2020 22:11:31: 5000000 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, 15 Apr 2020 22:11:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5702592/SRX5702592.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5702592/SRX5702592.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5702592/SRX5702592.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5702592/SRX5702592.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 15 Apr 2020 22:11:33: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:11:33: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:11:37: 6000000 INFO @ Wed, 15 Apr 2020 22:11:39: 1000000 INFO @ Wed, 15 Apr 2020 22:11:43: 7000000 INFO @ Wed, 15 Apr 2020 22:11:44: 2000000 INFO @ Wed, 15 Apr 2020 22:11:48: 8000000 INFO @ Wed, 15 Apr 2020 22:11:49: 3000000 INFO @ Wed, 15 Apr 2020 22:11:54: 9000000 INFO @ Wed, 15 Apr 2020 22:11:55: 4000000 INFO @ Wed, 15 Apr 2020 22:12:00: 10000000 INFO @ Wed, 15 Apr 2020 22:12:00: 5000000 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, 15 Apr 2020 22:12:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5702592/SRX5702592.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5702592/SRX5702592.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5702592/SRX5702592.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5702592/SRX5702592.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 15 Apr 2020 22:12:03: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:12:03: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:12:05: 11000000 INFO @ Wed, 15 Apr 2020 22:12:06: 6000000 INFO @ Wed, 15 Apr 2020 22:12:09: 1000000 INFO @ Wed, 15 Apr 2020 22:12:11: 7000000 INFO @ Wed, 15 Apr 2020 22:12:11: 12000000 INFO @ Wed, 15 Apr 2020 22:12:15: 2000000 INFO @ Wed, 15 Apr 2020 22:12:16: 8000000 INFO @ Wed, 15 Apr 2020 22:12:17: 13000000 INFO @ Wed, 15 Apr 2020 22:12:20: 3000000 INFO @ Wed, 15 Apr 2020 22:12:22: 9000000 INFO @ Wed, 15 Apr 2020 22:12:23: 14000000 INFO @ Wed, 15 Apr 2020 22:12:26: 4000000 INFO @ Wed, 15 Apr 2020 22:12:27: 10000000 INFO @ Wed, 15 Apr 2020 22:12:29: 15000000 INFO @ Wed, 15 Apr 2020 22:12:32: 5000000 INFO @ Wed, 15 Apr 2020 22:12:33: 11000000 INFO @ Wed, 15 Apr 2020 22:12:35: 16000000 INFO @ Wed, 15 Apr 2020 22:12:37: 6000000 INFO @ Wed, 15 Apr 2020 22:12:38: 12000000 INFO @ Wed, 15 Apr 2020 22:12:40: 17000000 INFO @ Wed, 15 Apr 2020 22:12:43: 7000000 INFO @ Wed, 15 Apr 2020 22:12:43: 13000000 INFO @ Wed, 15 Apr 2020 22:12:46: 18000000 INFO @ Wed, 15 Apr 2020 22:12:48: 14000000 INFO @ Wed, 15 Apr 2020 22:12:49: 8000000 INFO @ Wed, 15 Apr 2020 22:12:52: 19000000 INFO @ Wed, 15 Apr 2020 22:12:54: 15000000 INFO @ Wed, 15 Apr 2020 22:12:54: 9000000 INFO @ Wed, 15 Apr 2020 22:12:57: 20000000 INFO @ Wed, 15 Apr 2020 22:12:59: 16000000 INFO @ Wed, 15 Apr 2020 22:13:00: 10000000 INFO @ Wed, 15 Apr 2020 22:13:03: 21000000 INFO @ Wed, 15 Apr 2020 22:13:04: 17000000 INFO @ Wed, 15 Apr 2020 22:13:06: 11000000 INFO @ Wed, 15 Apr 2020 22:13:09: 22000000 INFO @ Wed, 15 Apr 2020 22:13:09: 18000000 INFO @ Wed, 15 Apr 2020 22:13:11: 12000000 INFO @ Wed, 15 Apr 2020 22:13:15: 23000000 INFO @ Wed, 15 Apr 2020 22:13:15: 19000000 INFO @ Wed, 15 Apr 2020 22:13:17: 13000000 INFO @ Wed, 15 Apr 2020 22:13:20: 20000000 INFO @ Wed, 15 Apr 2020 22:13:20: 24000000 INFO @ Wed, 15 Apr 2020 22:13:23: 14000000 INFO @ Wed, 15 Apr 2020 22:13:25: 21000000 INFO @ Wed, 15 Apr 2020 22:13:26: 25000000 INFO @ Wed, 15 Apr 2020 22:13:28: 15000000 INFO @ Wed, 15 Apr 2020 22:13:31: 22000000 INFO @ Wed, 15 Apr 2020 22:13:32: 26000000 INFO @ Wed, 15 Apr 2020 22:13:34: 16000000 INFO @ Wed, 15 Apr 2020 22:13:36: 23000000 INFO @ Wed, 15 Apr 2020 22:13:37: 27000000 INFO @ Wed, 15 Apr 2020 22:13:40: 17000000 INFO @ Wed, 15 Apr 2020 22:13:41: 24000000 INFO @ Wed, 15 Apr 2020 22:13:42: #1 tag size is determined as 60 bps INFO @ Wed, 15 Apr 2020 22:13:42: #1 tag size = 60 INFO @ Wed, 15 Apr 2020 22:13:42: #1 total tags in treatment: 27672878 INFO @ Wed, 15 Apr 2020 22:13:42: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:13:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:13:42: #1 tags after filtering in treatment: 27672878 INFO @ Wed, 15 Apr 2020 22:13:42: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:13:42: #1 finished! INFO @ Wed, 15 Apr 2020 22:13:42: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:13:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:13:44: #2 number of paired peaks: 167 WARNING @ Wed, 15 Apr 2020 22:13:44: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Wed, 15 Apr 2020 22:13:44: start model_add_line... INFO @ Wed, 15 Apr 2020 22:13:44: start X-correlation... INFO @ Wed, 15 Apr 2020 22:13:44: end of X-cor INFO @ Wed, 15 Apr 2020 22:13:44: #2 finished! INFO @ Wed, 15 Apr 2020 22:13:44: #2 predicted fragment length is 1 bps INFO @ Wed, 15 Apr 2020 22:13:44: #2 alternative fragment length(s) may be 1,39,569 bps INFO @ Wed, 15 Apr 2020 22:13:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5702592/SRX5702592.05_model.r WARNING @ Wed, 15 Apr 2020 22:13:44: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 22:13:44: #2 You may need to consider one of the other alternative d(s): 1,39,569 WARNING @ Wed, 15 Apr 2020 22:13:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 22:13:44: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:13:44: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:13:45: 18000000 INFO @ Wed, 15 Apr 2020 22:13:46: 25000000 INFO @ Wed, 15 Apr 2020 22:13:51: 19000000 INFO @ Wed, 15 Apr 2020 22:13:51: 26000000 INFO @ Wed, 15 Apr 2020 22:13:56: 27000000 INFO @ Wed, 15 Apr 2020 22:13:57: 20000000 INFO @ Wed, 15 Apr 2020 22:14:00: #1 tag size is determined as 60 bps INFO @ Wed, 15 Apr 2020 22:14:00: #1 tag size = 60 INFO @ Wed, 15 Apr 2020 22:14:00: #1 total tags in treatment: 27672878 INFO @ Wed, 15 Apr 2020 22:14:00: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:14:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:14:00: #1 tags after filtering in treatment: 27672878 INFO @ Wed, 15 Apr 2020 22:14:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:14:00: #1 finished! INFO @ Wed, 15 Apr 2020 22:14:00: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:14:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:14:02: 21000000 INFO @ Wed, 15 Apr 2020 22:14:02: #2 number of paired peaks: 167 WARNING @ Wed, 15 Apr 2020 22:14:02: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Wed, 15 Apr 2020 22:14:02: start model_add_line... INFO @ Wed, 15 Apr 2020 22:14:02: start X-correlation... INFO @ Wed, 15 Apr 2020 22:14:02: end of X-cor INFO @ Wed, 15 Apr 2020 22:14:02: #2 finished! INFO @ Wed, 15 Apr 2020 22:14:02: #2 predicted fragment length is 1 bps INFO @ Wed, 15 Apr 2020 22:14:02: #2 alternative fragment length(s) may be 1,39,569 bps INFO @ Wed, 15 Apr 2020 22:14:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5702592/SRX5702592.10_model.r WARNING @ Wed, 15 Apr 2020 22:14:02: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 22:14:02: #2 You may need to consider one of the other alternative d(s): 1,39,569 WARNING @ Wed, 15 Apr 2020 22:14:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 22:14:02: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:14:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:14:08: 22000000 INFO @ Wed, 15 Apr 2020 22:14:13: 23000000 INFO @ Wed, 15 Apr 2020 22:14:19: 24000000 INFO @ Wed, 15 Apr 2020 22:14:21: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:14:24: 25000000 INFO @ Wed, 15 Apr 2020 22:14:30: 26000000 INFO @ Wed, 15 Apr 2020 22:14:35: 27000000 INFO @ Wed, 15 Apr 2020 22:14:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5702592/SRX5702592.05_peaks.xls INFO @ Wed, 15 Apr 2020 22:14:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5702592/SRX5702592.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:14:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5702592/SRX5702592.05_summits.bed INFO @ Wed, 15 Apr 2020 22:14:38: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 22:14:39: #1 tag size is determined as 60 bps INFO @ Wed, 15 Apr 2020 22:14:39: #1 tag size = 60 INFO @ Wed, 15 Apr 2020 22:14:39: #1 total tags in treatment: 27672878 INFO @ Wed, 15 Apr 2020 22:14:39: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:14:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:14:40: #1 tags after filtering in treatment: 27672878 INFO @ Wed, 15 Apr 2020 22:14:40: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:14:40: #1 finished! INFO @ Wed, 15 Apr 2020 22:14:40: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:14:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:14:40: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:14:41: #2 number of paired peaks: 167 WARNING @ Wed, 15 Apr 2020 22:14:41: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Wed, 15 Apr 2020 22:14:41: start model_add_line... INFO @ Wed, 15 Apr 2020 22:14:41: start X-correlation... INFO @ Wed, 15 Apr 2020 22:14:41: end of X-cor INFO @ Wed, 15 Apr 2020 22:14:41: #2 finished! INFO @ Wed, 15 Apr 2020 22:14:41: #2 predicted fragment length is 1 bps INFO @ Wed, 15 Apr 2020 22:14:41: #2 alternative fragment length(s) may be 1,39,569 bps INFO @ Wed, 15 Apr 2020 22:14:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5702592/SRX5702592.20_model.r WARNING @ Wed, 15 Apr 2020 22:14:41: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 22:14:41: #2 You may need to consider one of the other alternative d(s): 1,39,569 WARNING @ Wed, 15 Apr 2020 22:14:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 22:14:41: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:14:41: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:14:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5702592/SRX5702592.10_peaks.xls INFO @ Wed, 15 Apr 2020 22:14:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5702592/SRX5702592.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:14:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5702592/SRX5702592.10_summits.bed INFO @ Wed, 15 Apr 2020 22:14:57: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 22:15:19: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:15:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5702592/SRX5702592.20_peaks.xls INFO @ Wed, 15 Apr 2020 22:15:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5702592/SRX5702592.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:15:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5702592/SRX5702592.20_summits.bed INFO @ Wed, 15 Apr 2020 22:15:36: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。