Job ID = 6366283 SRX = SRX1078708 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:44:22 prefetch.2.10.7: 1) Downloading 'SRR2084315'... 2020-06-15T22:44:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:46:52 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:46:52 prefetch.2.10.7: 1) 'SRR2084315' was downloaded successfully Read 28713577 spots for SRR2084315/SRR2084315.sra Written 28713577 spots for SRR2084315/SRR2084315.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: 00:06:54 28713577 reads; of these: 28713577 (100.00%) were unpaired; of these: 762247 (2.65%) aligned 0 times 23455169 (81.69%) aligned exactly 1 time 4496161 (15.66%) aligned >1 times 97.35% overall alignment rate Time searching: 00:06:54 Overall time: 00:06:54 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] 4015860 / 27951330 = 0.1437 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 08:03:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078708/SRX1078708.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078708/SRX1078708.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078708/SRX1078708.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078708/SRX1078708.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 08:03:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:03:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:03:16: 1000000 INFO @ Tue, 16 Jun 2020 08:03:22: 2000000 INFO @ Tue, 16 Jun 2020 08:03:27: 3000000 INFO @ Tue, 16 Jun 2020 08:03:33: 4000000 INFO @ Tue, 16 Jun 2020 08:03:39: 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 08:03:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078708/SRX1078708.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078708/SRX1078708.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078708/SRX1078708.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078708/SRX1078708.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 08:03:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:03:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:03:44: 6000000 INFO @ Tue, 16 Jun 2020 08:03:47: 1000000 INFO @ Tue, 16 Jun 2020 08:03:50: 7000000 INFO @ Tue, 16 Jun 2020 08:03:53: 2000000 INFO @ Tue, 16 Jun 2020 08:03:56: 8000000 INFO @ Tue, 16 Jun 2020 08:03:59: 3000000 INFO @ Tue, 16 Jun 2020 08:04:02: 9000000 INFO @ Tue, 16 Jun 2020 08:04:05: 4000000 INFO @ Tue, 16 Jun 2020 08:04:08: 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 08:04:11: 5000000 INFO @ Tue, 16 Jun 2020 08:04:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078708/SRX1078708.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078708/SRX1078708.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078708/SRX1078708.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078708/SRX1078708.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 08:04:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:04:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:04:14: 11000000 INFO @ Tue, 16 Jun 2020 08:04:17: 6000000 INFO @ Tue, 16 Jun 2020 08:04:17: 1000000 INFO @ Tue, 16 Jun 2020 08:04:20: 12000000 INFO @ Tue, 16 Jun 2020 08:04:23: 7000000 INFO @ Tue, 16 Jun 2020 08:04:24: 2000000 INFO @ Tue, 16 Jun 2020 08:04:27: 13000000 INFO @ Tue, 16 Jun 2020 08:04:29: 8000000 INFO @ Tue, 16 Jun 2020 08:04:30: 3000000 INFO @ Tue, 16 Jun 2020 08:04:33: 14000000 INFO @ Tue, 16 Jun 2020 08:04:35: 9000000 INFO @ Tue, 16 Jun 2020 08:04:36: 4000000 INFO @ Tue, 16 Jun 2020 08:04:39: 15000000 INFO @ Tue, 16 Jun 2020 08:04:41: 10000000 INFO @ Tue, 16 Jun 2020 08:04:43: 5000000 INFO @ Tue, 16 Jun 2020 08:04:46: 16000000 INFO @ Tue, 16 Jun 2020 08:04:48: 11000000 INFO @ Tue, 16 Jun 2020 08:04:49: 6000000 INFO @ Tue, 16 Jun 2020 08:04:52: 17000000 INFO @ Tue, 16 Jun 2020 08:04:54: 12000000 INFO @ Tue, 16 Jun 2020 08:04:55: 7000000 INFO @ Tue, 16 Jun 2020 08:04:59: 18000000 INFO @ Tue, 16 Jun 2020 08:05:00: 13000000 INFO @ Tue, 16 Jun 2020 08:05:02: 8000000 INFO @ Tue, 16 Jun 2020 08:05:05: 19000000 INFO @ Tue, 16 Jun 2020 08:05:06: 14000000 INFO @ Tue, 16 Jun 2020 08:05:08: 9000000 INFO @ Tue, 16 Jun 2020 08:05:12: 20000000 INFO @ Tue, 16 Jun 2020 08:05:12: 15000000 INFO @ Tue, 16 Jun 2020 08:05:15: 10000000 INFO @ Tue, 16 Jun 2020 08:05:18: 21000000 INFO @ Tue, 16 Jun 2020 08:05:19: 16000000 INFO @ Tue, 16 Jun 2020 08:05:21: 11000000 INFO @ Tue, 16 Jun 2020 08:05:25: 17000000 INFO @ Tue, 16 Jun 2020 08:05:25: 22000000 INFO @ Tue, 16 Jun 2020 08:05:28: 12000000 INFO @ Tue, 16 Jun 2020 08:05:31: 18000000 INFO @ Tue, 16 Jun 2020 08:05:32: 23000000 INFO @ Tue, 16 Jun 2020 08:05:34: 13000000 INFO @ Tue, 16 Jun 2020 08:05:37: 19000000 INFO @ Tue, 16 Jun 2020 08:05:38: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:05:38: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:05:38: #1 total tags in treatment: 23935470 INFO @ Tue, 16 Jun 2020 08:05:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:05:38: #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 08:05:38: #1 tags after filtering in treatment: 23935470 INFO @ Tue, 16 Jun 2020 08:05:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:05:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:05:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:05:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:05:40: #2 number of paired peaks: 164 WARNING @ Tue, 16 Jun 2020 08:05:40: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Tue, 16 Jun 2020 08:05:40: start model_add_line... INFO @ Tue, 16 Jun 2020 08:05:40: start X-correlation... INFO @ Tue, 16 Jun 2020 08:05:40: end of X-cor INFO @ Tue, 16 Jun 2020 08:05:40: #2 finished! INFO @ Tue, 16 Jun 2020 08:05:40: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:05:40: #2 alternative fragment length(s) may be 1,22,51,542,592 bps INFO @ Tue, 16 Jun 2020 08:05:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078708/SRX1078708.05_model.r WARNING @ Tue, 16 Jun 2020 08:05:40: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:05:40: #2 You may need to consider one of the other alternative d(s): 1,22,51,542,592 WARNING @ Tue, 16 Jun 2020 08:05:40: #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 08:05:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:05:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:05:40: 14000000 INFO @ Tue, 16 Jun 2020 08:05:43: 20000000 INFO @ Tue, 16 Jun 2020 08:05:47: 15000000 INFO @ Tue, 16 Jun 2020 08:05:50: 21000000 INFO @ Tue, 16 Jun 2020 08:05:53: 16000000 INFO @ Tue, 16 Jun 2020 08:05:56: 22000000 INFO @ Tue, 16 Jun 2020 08:05:59: 17000000 INFO @ Tue, 16 Jun 2020 08:06:02: 23000000 INFO @ Tue, 16 Jun 2020 08:06:05: 18000000 INFO @ Tue, 16 Jun 2020 08:06:08: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:06:08: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:06:08: #1 total tags in treatment: 23935470 INFO @ Tue, 16 Jun 2020 08:06:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:08: #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 08:06:08: #1 tags after filtering in treatment: 23935470 INFO @ Tue, 16 Jun 2020 08:06:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:08: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:10: #2 number of paired peaks: 164 WARNING @ Tue, 16 Jun 2020 08:06:10: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Tue, 16 Jun 2020 08:06:10: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:10: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:10: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:10: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:10: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:06:10: #2 alternative fragment length(s) may be 1,22,51,542,592 bps INFO @ Tue, 16 Jun 2020 08:06:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078708/SRX1078708.10_model.r WARNING @ Tue, 16 Jun 2020 08:06:10: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:06:10: #2 You may need to consider one of the other alternative d(s): 1,22,51,542,592 WARNING @ Tue, 16 Jun 2020 08:06:10: #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 08:06:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:06:12: 19000000 INFO @ Tue, 16 Jun 2020 08:06:18: 20000000 INFO @ Tue, 16 Jun 2020 08:06:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:06:24: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:06:30: 22000000 INFO @ Tue, 16 Jun 2020 08:06:36: 23000000 INFO @ Tue, 16 Jun 2020 08:06:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078708/SRX1078708.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:06:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078708/SRX1078708.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:06:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078708/SRX1078708.05_summits.bed INFO @ Tue, 16 Jun 2020 08:06:40: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:06:41: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:06:41: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:06:41: #1 total tags in treatment: 23935470 INFO @ Tue, 16 Jun 2020 08:06:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:41: #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 08:06:42: #1 tags after filtering in treatment: 23935470 INFO @ Tue, 16 Jun 2020 08:06:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:42: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:43: #2 number of paired peaks: 164 WARNING @ Tue, 16 Jun 2020 08:06:43: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Tue, 16 Jun 2020 08:06:43: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:43: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:43: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:43: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:43: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:06:43: #2 alternative fragment length(s) may be 1,22,51,542,592 bps INFO @ Tue, 16 Jun 2020 08:06:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078708/SRX1078708.20_model.r WARNING @ Tue, 16 Jun 2020 08:06:43: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:06:43: #2 You may need to consider one of the other alternative d(s): 1,22,51,542,592 WARNING @ Tue, 16 Jun 2020 08:06:43: #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 08:06:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:06:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:07:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078708/SRX1078708.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078708/SRX1078708.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078708/SRX1078708.10_summits.bed INFO @ Tue, 16 Jun 2020 08:07:09: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:07:23: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:07:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078708/SRX1078708.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078708/SRX1078708.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078708/SRX1078708.20_summits.bed INFO @ Tue, 16 Jun 2020 08:07:42: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling