Job ID = 6367028 SRX = SRX2737087 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:14:01 prefetch.2.10.7: 1) Downloading 'SRR5448125'... 2020-06-15T23:14:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:15:48 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:15:48 prefetch.2.10.7: 1) 'SRR5448125' was downloaded successfully 2020-06-15T23:15:48 prefetch.2.10.7: 'SRR5448125' has 0 unresolved dependencies Read 32014644 spots for SRR5448125/SRR5448125.sra Written 32014644 spots for SRR5448125/SRR5448125.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: 00:07:25 32014644 reads; of these: 32014644 (100.00%) were unpaired; of these: 636422 (1.99%) aligned 0 times 26437759 (82.58%) aligned exactly 1 time 4940463 (15.43%) aligned >1 times 98.01% overall alignment rate Time searching: 00:07:25 Overall time: 00:07:25 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 16 files... [bam_rmdupse_core] 4527591 / 31378222 = 0.1443 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 08:30:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2737087/SRX2737087.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2737087/SRX2737087.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2737087/SRX2737087.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2737087/SRX2737087.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 08:30:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:30:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:30:41: 1000000 INFO @ Tue, 16 Jun 2020 08:30:46: 2000000 INFO @ Tue, 16 Jun 2020 08:30:51: 3000000 INFO @ Tue, 16 Jun 2020 08:30:56: 4000000 INFO @ Tue, 16 Jun 2020 08:31:01: 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 08:31:06: 6000000 INFO @ Tue, 16 Jun 2020 08:31:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2737087/SRX2737087.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2737087/SRX2737087.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2737087/SRX2737087.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2737087/SRX2737087.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 08:31:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:11: 7000000 INFO @ Tue, 16 Jun 2020 08:31:11: 1000000 INFO @ Tue, 16 Jun 2020 08:31:17: 8000000 INFO @ Tue, 16 Jun 2020 08:31:17: 2000000 INFO @ Tue, 16 Jun 2020 08:31:22: 9000000 INFO @ Tue, 16 Jun 2020 08:31:22: 3000000 INFO @ Tue, 16 Jun 2020 08:31:27: 10000000 INFO @ Tue, 16 Jun 2020 08:31:28: 4000000 INFO @ Tue, 16 Jun 2020 08:31:33: 11000000 INFO @ Tue, 16 Jun 2020 08:31:33: 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 @ Tue, 16 Jun 2020 08:31:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2737087/SRX2737087.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2737087/SRX2737087.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2737087/SRX2737087.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2737087/SRX2737087.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 08:31:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:38: 12000000 INFO @ Tue, 16 Jun 2020 08:31:39: 6000000 INFO @ Tue, 16 Jun 2020 08:31:42: 1000000 INFO @ Tue, 16 Jun 2020 08:31:44: 13000000 INFO @ Tue, 16 Jun 2020 08:31:44: 7000000 INFO @ Tue, 16 Jun 2020 08:31:47: 2000000 INFO @ Tue, 16 Jun 2020 08:31:49: 14000000 INFO @ Tue, 16 Jun 2020 08:31:50: 8000000 INFO @ Tue, 16 Jun 2020 08:31:53: 3000000 INFO @ Tue, 16 Jun 2020 08:31:55: 15000000 INFO @ Tue, 16 Jun 2020 08:31:56: 9000000 INFO @ Tue, 16 Jun 2020 08:31:58: 4000000 INFO @ Tue, 16 Jun 2020 08:32:00: 16000000 INFO @ Tue, 16 Jun 2020 08:32:01: 10000000 INFO @ Tue, 16 Jun 2020 08:32:04: 5000000 INFO @ Tue, 16 Jun 2020 08:32:06: 17000000 INFO @ Tue, 16 Jun 2020 08:32:07: 11000000 INFO @ Tue, 16 Jun 2020 08:32:09: 6000000 INFO @ Tue, 16 Jun 2020 08:32:11: 18000000 INFO @ Tue, 16 Jun 2020 08:32:12: 12000000 INFO @ Tue, 16 Jun 2020 08:32:15: 7000000 INFO @ Tue, 16 Jun 2020 08:32:16: 19000000 INFO @ Tue, 16 Jun 2020 08:32:17: 13000000 INFO @ Tue, 16 Jun 2020 08:32:20: 8000000 INFO @ Tue, 16 Jun 2020 08:32:22: 20000000 INFO @ Tue, 16 Jun 2020 08:32:23: 14000000 INFO @ Tue, 16 Jun 2020 08:32:25: 9000000 INFO @ Tue, 16 Jun 2020 08:32:27: 21000000 INFO @ Tue, 16 Jun 2020 08:32:28: 15000000 INFO @ Tue, 16 Jun 2020 08:32:31: 10000000 INFO @ Tue, 16 Jun 2020 08:32:33: 22000000 INFO @ Tue, 16 Jun 2020 08:32:34: 16000000 INFO @ Tue, 16 Jun 2020 08:32:36: 11000000 INFO @ Tue, 16 Jun 2020 08:32:38: 23000000 INFO @ Tue, 16 Jun 2020 08:32:39: 17000000 INFO @ Tue, 16 Jun 2020 08:32:42: 12000000 INFO @ Tue, 16 Jun 2020 08:32:44: 24000000 INFO @ Tue, 16 Jun 2020 08:32:45: 18000000 INFO @ Tue, 16 Jun 2020 08:32:47: 13000000 INFO @ Tue, 16 Jun 2020 08:32:49: 25000000 INFO @ Tue, 16 Jun 2020 08:32:50: 19000000 INFO @ Tue, 16 Jun 2020 08:32:53: 14000000 INFO @ Tue, 16 Jun 2020 08:32:55: 26000000 INFO @ Tue, 16 Jun 2020 08:32:56: 20000000 INFO @ Tue, 16 Jun 2020 08:32:58: 15000000 INFO @ Tue, 16 Jun 2020 08:32:59: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:32:59: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:32:59: #1 total tags in treatment: 26850631 INFO @ Tue, 16 Jun 2020 08:32:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:59: #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 08:33:00: #1 tags after filtering in treatment: 26850631 INFO @ Tue, 16 Jun 2020 08:33:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:33:00: #1 finished! INFO @ Tue, 16 Jun 2020 08:33:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:33:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:33:01: 21000000 INFO @ Tue, 16 Jun 2020 08:33:01: #2 number of paired peaks: 106 WARNING @ Tue, 16 Jun 2020 08:33:01: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Tue, 16 Jun 2020 08:33:01: start model_add_line... INFO @ Tue, 16 Jun 2020 08:33:02: start X-correlation... INFO @ Tue, 16 Jun 2020 08:33:02: end of X-cor INFO @ Tue, 16 Jun 2020 08:33:02: #2 finished! INFO @ Tue, 16 Jun 2020 08:33:02: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:33:02: #2 alternative fragment length(s) may be 1,47,447,459,509 bps INFO @ Tue, 16 Jun 2020 08:33:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2737087/SRX2737087.05_model.r WARNING @ Tue, 16 Jun 2020 08:33:02: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:33:02: #2 You may need to consider one of the other alternative d(s): 1,47,447,459,509 WARNING @ Tue, 16 Jun 2020 08:33:02: #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 08:33:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:33:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:33:03: 16000000 INFO @ Tue, 16 Jun 2020 08:33:06: 22000000 INFO @ Tue, 16 Jun 2020 08:33:09: 17000000 INFO @ Tue, 16 Jun 2020 08:33:12: 23000000 INFO @ Tue, 16 Jun 2020 08:33:14: 18000000 INFO @ Tue, 16 Jun 2020 08:33:17: 24000000 INFO @ Tue, 16 Jun 2020 08:33:20: 19000000 INFO @ Tue, 16 Jun 2020 08:33:23: 25000000 INFO @ Tue, 16 Jun 2020 08:33:25: 20000000 INFO @ Tue, 16 Jun 2020 08:33:28: 26000000 INFO @ Tue, 16 Jun 2020 08:33:30: 21000000 INFO @ Tue, 16 Jun 2020 08:33:32: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:33:32: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:33:32: #1 total tags in treatment: 26850631 INFO @ Tue, 16 Jun 2020 08:33:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:33:32: #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 08:33:33: #1 tags after filtering in treatment: 26850631 INFO @ Tue, 16 Jun 2020 08:33:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:33:33: #1 finished! INFO @ Tue, 16 Jun 2020 08:33:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:33:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:33:35: #2 number of paired peaks: 106 WARNING @ Tue, 16 Jun 2020 08:33:35: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Tue, 16 Jun 2020 08:33:35: start model_add_line... INFO @ Tue, 16 Jun 2020 08:33:35: start X-correlation... INFO @ Tue, 16 Jun 2020 08:33:35: end of X-cor INFO @ Tue, 16 Jun 2020 08:33:35: #2 finished! INFO @ Tue, 16 Jun 2020 08:33:35: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:33:35: #2 alternative fragment length(s) may be 1,47,447,459,509 bps INFO @ Tue, 16 Jun 2020 08:33:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2737087/SRX2737087.10_model.r WARNING @ Tue, 16 Jun 2020 08:33:35: #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 08:33:35: #2 You may need to consider one of the other alternative d(s): 1,47,447,459,509 WARNING @ Tue, 16 Jun 2020 08:33:35: #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 08:33:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:33:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:33:35: 22000000 INFO @ Tue, 16 Jun 2020 08:33:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:33:41: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:33:46: 24000000 INFO @ Tue, 16 Jun 2020 08:33:51: 25000000 INFO @ Tue, 16 Jun 2020 08:33:56: 26000000 INFO @ Tue, 16 Jun 2020 08:33:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2737087/SRX2737087.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:33:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2737087/SRX2737087.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:33:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2737087/SRX2737087.05_summits.bed INFO @ Tue, 16 Jun 2020 08:33:57: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:34:00: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:34:00: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:34:00: #1 total tags in treatment: 26850631 INFO @ Tue, 16 Jun 2020 08:34:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:34:00: #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 08:34:00: #1 tags after filtering in treatment: 26850631 INFO @ Tue, 16 Jun 2020 08:34:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:34:00: #1 finished! INFO @ Tue, 16 Jun 2020 08:34:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:34:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:34:02: #2 number of paired peaks: 106 WARNING @ Tue, 16 Jun 2020 08:34:02: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Tue, 16 Jun 2020 08:34:02: start model_add_line... INFO @ Tue, 16 Jun 2020 08:34:02: start X-correlation... INFO @ Tue, 16 Jun 2020 08:34:02: end of X-cor INFO @ Tue, 16 Jun 2020 08:34:02: #2 finished! INFO @ Tue, 16 Jun 2020 08:34:02: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:34:02: #2 alternative fragment length(s) may be 1,47,447,459,509 bps INFO @ Tue, 16 Jun 2020 08:34:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2737087/SRX2737087.20_model.r WARNING @ Tue, 16 Jun 2020 08:34:02: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:34:02: #2 You may need to consider one of the other alternative d(s): 1,47,447,459,509 WARNING @ Tue, 16 Jun 2020 08:34:02: #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 08:34:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:34:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:34:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:34:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2737087/SRX2737087.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:34:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2737087/SRX2737087.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:34:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2737087/SRX2737087.10_summits.bed INFO @ Tue, 16 Jun 2020 08:34:28: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:34:39: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:34:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2737087/SRX2737087.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:34:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2737087/SRX2737087.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:34:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2737087/SRX2737087.20_summits.bed INFO @ Tue, 16 Jun 2020 08:34:56: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling