Job ID = 6368578 SRX = SRX5020804 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:20:21 prefetch.2.10.7: 1) Downloading 'SRR8201427'... 2020-06-16T00:20:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:23:26 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:23:26 prefetch.2.10.7: 1) 'SRR8201427' was downloaded successfully 2020-06-16T00:23:26 prefetch.2.10.7: 'SRR8201427' has 0 unresolved dependencies Read 27576294 spots for SRR8201427/SRR8201427.sra Written 27576294 spots for SRR8201427/SRR8201427.sra 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: 00:08:52 27576294 reads; of these: 27576294 (100.00%) were unpaired; of these: 1198951 (4.35%) aligned 0 times 22043779 (79.94%) aligned exactly 1 time 4333564 (15.71%) aligned >1 times 95.65% overall alignment rate Time searching: 00:08:52 Overall time: 00:08:52 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 12 files... [bam_rmdupse_core] 4138357 / 26377343 = 0.1569 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 @ Tue, 16 Jun 2020 09:40:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020804/SRX5020804.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020804/SRX5020804.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020804/SRX5020804.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020804/SRX5020804.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 @ Tue, 16 Jun 2020 09:40:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:30: 1000000 INFO @ Tue, 16 Jun 2020 09:40:36: 2000000 INFO @ Tue, 16 Jun 2020 09:40:41: 3000000 INFO @ Tue, 16 Jun 2020 09:40:47: 4000000 INFO @ Tue, 16 Jun 2020 09:40:53: 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 @ Tue, 16 Jun 2020 09:40:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020804/SRX5020804.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020804/SRX5020804.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020804/SRX5020804.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020804/SRX5020804.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 @ Tue, 16 Jun 2020 09:40:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:58: 6000000 INFO @ Tue, 16 Jun 2020 09:41:01: 1000000 INFO @ Tue, 16 Jun 2020 09:41:04: 7000000 INFO @ Tue, 16 Jun 2020 09:41:07: 2000000 INFO @ Tue, 16 Jun 2020 09:41:10: 8000000 INFO @ Tue, 16 Jun 2020 09:41:13: 3000000 INFO @ Tue, 16 Jun 2020 09:41:16: 9000000 INFO @ Tue, 16 Jun 2020 09:41:19: 4000000 INFO @ Tue, 16 Jun 2020 09:41:22: 10000000 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 @ Tue, 16 Jun 2020 09:41:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020804/SRX5020804.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020804/SRX5020804.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020804/SRX5020804.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020804/SRX5020804.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 @ Tue, 16 Jun 2020 09:41:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:41:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:41:25: 5000000 INFO @ Tue, 16 Jun 2020 09:41:28: 11000000 INFO @ Tue, 16 Jun 2020 09:41:31: 6000000 INFO @ Tue, 16 Jun 2020 09:41:31: 1000000 INFO @ Tue, 16 Jun 2020 09:41:35: 12000000 INFO @ Tue, 16 Jun 2020 09:41:37: 7000000 INFO @ Tue, 16 Jun 2020 09:41:38: 2000000 INFO @ Tue, 16 Jun 2020 09:41:41: 13000000 INFO @ Tue, 16 Jun 2020 09:41:44: 8000000 INFO @ Tue, 16 Jun 2020 09:41:44: 3000000 INFO @ Tue, 16 Jun 2020 09:41:47: 14000000 INFO @ Tue, 16 Jun 2020 09:41:50: 9000000 INFO @ Tue, 16 Jun 2020 09:41:50: 4000000 INFO @ Tue, 16 Jun 2020 09:41:53: 15000000 INFO @ Tue, 16 Jun 2020 09:41:56: 10000000 INFO @ Tue, 16 Jun 2020 09:41:56: 5000000 INFO @ Tue, 16 Jun 2020 09:41:59: 16000000 INFO @ Tue, 16 Jun 2020 09:42:02: 11000000 INFO @ Tue, 16 Jun 2020 09:42:02: 6000000 INFO @ Tue, 16 Jun 2020 09:42:05: 17000000 INFO @ Tue, 16 Jun 2020 09:42:08: 12000000 INFO @ Tue, 16 Jun 2020 09:42:09: 7000000 INFO @ Tue, 16 Jun 2020 09:42:12: 18000000 INFO @ Tue, 16 Jun 2020 09:42:15: 13000000 INFO @ Tue, 16 Jun 2020 09:42:15: 8000000 INFO @ Tue, 16 Jun 2020 09:42:18: 19000000 INFO @ Tue, 16 Jun 2020 09:42:21: 14000000 INFO @ Tue, 16 Jun 2020 09:42:21: 9000000 INFO @ Tue, 16 Jun 2020 09:42:24: 20000000 INFO @ Tue, 16 Jun 2020 09:42:27: 15000000 INFO @ Tue, 16 Jun 2020 09:42:27: 10000000 INFO @ Tue, 16 Jun 2020 09:42:30: 21000000 INFO @ Tue, 16 Jun 2020 09:42:33: 16000000 INFO @ Tue, 16 Jun 2020 09:42:33: 11000000 INFO @ Tue, 16 Jun 2020 09:42:36: 22000000 INFO @ Tue, 16 Jun 2020 09:42:37: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:42:37: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:42:37: #1 total tags in treatment: 22238986 INFO @ Tue, 16 Jun 2020 09:42:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:42:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:42:38: #1 tags after filtering in treatment: 22238986 INFO @ Tue, 16 Jun 2020 09:42:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:42:38: #1 finished! INFO @ Tue, 16 Jun 2020 09:42:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:42:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:42:39: 17000000 INFO @ Tue, 16 Jun 2020 09:42:39: #2 number of paired peaks: 185 WARNING @ Tue, 16 Jun 2020 09:42:39: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Tue, 16 Jun 2020 09:42:39: start model_add_line... INFO @ Tue, 16 Jun 2020 09:42:39: 12000000 INFO @ Tue, 16 Jun 2020 09:42:39: start X-correlation... INFO @ Tue, 16 Jun 2020 09:42:39: end of X-cor INFO @ Tue, 16 Jun 2020 09:42:39: #2 finished! INFO @ Tue, 16 Jun 2020 09:42:39: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:42:39: #2 alternative fragment length(s) may be 2,38,551 bps INFO @ Tue, 16 Jun 2020 09:42:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020804/SRX5020804.05_model.r WARNING @ Tue, 16 Jun 2020 09:42:39: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:42:39: #2 You may need to consider one of the other alternative d(s): 2,38,551 WARNING @ Tue, 16 Jun 2020 09:42:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:42:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:42:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:42:45: 18000000 INFO @ Tue, 16 Jun 2020 09:42:45: 13000000 INFO @ Tue, 16 Jun 2020 09:42:51: 19000000 INFO @ Tue, 16 Jun 2020 09:42:51: 14000000 INFO @ Tue, 16 Jun 2020 09:42:57: 20000000 INFO @ Tue, 16 Jun 2020 09:42:57: 15000000 INFO @ Tue, 16 Jun 2020 09:43:03: 21000000 INFO @ Tue, 16 Jun 2020 09:43:03: 16000000 INFO @ Tue, 16 Jun 2020 09:43:09: 22000000 INFO @ Tue, 16 Jun 2020 09:43:09: 17000000 INFO @ Tue, 16 Jun 2020 09:43:10: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:43:10: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:43:10: #1 total tags in treatment: 22238986 INFO @ Tue, 16 Jun 2020 09:43:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:43:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:43:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:43:11: #1 tags after filtering in treatment: 22238986 INFO @ Tue, 16 Jun 2020 09:43:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:43:11: #1 finished! INFO @ Tue, 16 Jun 2020 09:43:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:43:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:43:12: #2 number of paired peaks: 185 WARNING @ Tue, 16 Jun 2020 09:43:12: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Tue, 16 Jun 2020 09:43:12: start model_add_line... INFO @ Tue, 16 Jun 2020 09:43:12: start X-correlation... INFO @ Tue, 16 Jun 2020 09:43:12: end of X-cor INFO @ Tue, 16 Jun 2020 09:43:12: #2 finished! INFO @ Tue, 16 Jun 2020 09:43:12: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:43:12: #2 alternative fragment length(s) may be 2,38,551 bps INFO @ Tue, 16 Jun 2020 09:43:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020804/SRX5020804.10_model.r WARNING @ Tue, 16 Jun 2020 09:43:12: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:43:12: #2 You may need to consider one of the other alternative d(s): 2,38,551 WARNING @ Tue, 16 Jun 2020 09:43:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:43:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:43:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:43:15: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:43:21: 19000000 INFO @ Tue, 16 Jun 2020 09:43:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020804/SRX5020804.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:43:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020804/SRX5020804.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:43:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020804/SRX5020804.05_summits.bed INFO @ Tue, 16 Jun 2020 09:43:26: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:43:27: 20000000 INFO @ Tue, 16 Jun 2020 09:43:33: 21000000 INFO @ Tue, 16 Jun 2020 09:43:39: 22000000 INFO @ Tue, 16 Jun 2020 09:43:40: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:43:40: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:43:40: #1 total tags in treatment: 22238986 INFO @ Tue, 16 Jun 2020 09:43:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:43:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:43:41: #1 tags after filtering in treatment: 22238986 INFO @ Tue, 16 Jun 2020 09:43:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:43:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:43:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:43:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:43:42: #2 number of paired peaks: 185 WARNING @ Tue, 16 Jun 2020 09:43:42: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Tue, 16 Jun 2020 09:43:42: start model_add_line... INFO @ Tue, 16 Jun 2020 09:43:42: start X-correlation... INFO @ Tue, 16 Jun 2020 09:43:42: end of X-cor INFO @ Tue, 16 Jun 2020 09:43:42: #2 finished! INFO @ Tue, 16 Jun 2020 09:43:42: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:43:42: #2 alternative fragment length(s) may be 2,38,551 bps INFO @ Tue, 16 Jun 2020 09:43:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020804/SRX5020804.20_model.r WARNING @ Tue, 16 Jun 2020 09:43:42: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:43:42: #2 You may need to consider one of the other alternative d(s): 2,38,551 WARNING @ Tue, 16 Jun 2020 09:43:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:43:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:43:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:43:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:44:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020804/SRX5020804.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:44:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020804/SRX5020804.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:44:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020804/SRX5020804.10_summits.bed INFO @ Tue, 16 Jun 2020 09:44:00: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:44:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:44:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020804/SRX5020804.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:44:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020804/SRX5020804.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:44:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020804/SRX5020804.20_summits.bed INFO @ Tue, 16 Jun 2020 09:44:30: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling