Job ID = 6366745 SRX = SRX2228898 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:03:53 prefetch.2.10.7: 1) Downloading 'SRR4380354'... 2020-06-15T23:03:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:05:11 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:05:12 prefetch.2.10.7: 'SRR4380354' is valid 2020-06-15T23:05:12 prefetch.2.10.7: 1) 'SRR4380354' was downloaded successfully Read 28110258 spots for SRR4380354/SRR4380354.sra Written 28110258 spots for SRR4380354/SRR4380354.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: 00:04:44 28110258 reads; of these: 28110258 (100.00%) were unpaired; of these: 347156 (1.23%) aligned 0 times 22851895 (81.29%) aligned exactly 1 time 4911207 (17.47%) aligned >1 times 98.77% overall alignment rate Time searching: 00:04:44 Overall time: 00:04:44 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 8 files... [bam_rmdupse_core] 5006531 / 27763102 = 0.1803 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 08:16:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228898/SRX2228898.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228898/SRX2228898.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228898/SRX2228898.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228898/SRX2228898.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 08:16:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:16:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:17:00: 1000000 INFO @ Tue, 16 Jun 2020 08:17:05: 2000000 INFO @ Tue, 16 Jun 2020 08:17:11: 3000000 INFO @ Tue, 16 Jun 2020 08:17:16: 4000000 INFO @ Tue, 16 Jun 2020 08:17:22: 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 08:17:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228898/SRX2228898.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228898/SRX2228898.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228898/SRX2228898.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228898/SRX2228898.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 08:17:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:17:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:17:27: 6000000 INFO @ Tue, 16 Jun 2020 08:17:30: 1000000 INFO @ Tue, 16 Jun 2020 08:17:32: 7000000 INFO @ Tue, 16 Jun 2020 08:17:36: 2000000 INFO @ Tue, 16 Jun 2020 08:17:38: 8000000 INFO @ Tue, 16 Jun 2020 08:17:41: 3000000 INFO @ Tue, 16 Jun 2020 08:17:43: 9000000 INFO @ Tue, 16 Jun 2020 08:17:47: 4000000 INFO @ Tue, 16 Jun 2020 08:17:49: 10000000 INFO @ Tue, 16 Jun 2020 08:17:52: 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 08:17:55: 11000000 INFO @ Tue, 16 Jun 2020 08:17:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228898/SRX2228898.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228898/SRX2228898.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228898/SRX2228898.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228898/SRX2228898.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 08:17:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:17:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:17:58: 6000000 INFO @ Tue, 16 Jun 2020 08:18:00: 12000000 INFO @ Tue, 16 Jun 2020 08:18:00: 1000000 INFO @ Tue, 16 Jun 2020 08:18:03: 7000000 INFO @ Tue, 16 Jun 2020 08:18:06: 13000000 INFO @ Tue, 16 Jun 2020 08:18:06: 2000000 INFO @ Tue, 16 Jun 2020 08:18:09: 8000000 INFO @ Tue, 16 Jun 2020 08:18:12: 3000000 INFO @ Tue, 16 Jun 2020 08:18:12: 14000000 INFO @ Tue, 16 Jun 2020 08:18:14: 9000000 INFO @ Tue, 16 Jun 2020 08:18:17: 4000000 INFO @ Tue, 16 Jun 2020 08:18:17: 15000000 INFO @ Tue, 16 Jun 2020 08:18:20: 10000000 INFO @ Tue, 16 Jun 2020 08:18:23: 5000000 INFO @ Tue, 16 Jun 2020 08:18:23: 16000000 INFO @ Tue, 16 Jun 2020 08:18:25: 11000000 INFO @ Tue, 16 Jun 2020 08:18:28: 6000000 INFO @ Tue, 16 Jun 2020 08:18:28: 17000000 INFO @ Tue, 16 Jun 2020 08:18:31: 12000000 INFO @ Tue, 16 Jun 2020 08:18:33: 7000000 INFO @ Tue, 16 Jun 2020 08:18:34: 18000000 INFO @ Tue, 16 Jun 2020 08:18:37: 13000000 INFO @ Tue, 16 Jun 2020 08:18:39: 19000000 INFO @ Tue, 16 Jun 2020 08:18:39: 8000000 INFO @ Tue, 16 Jun 2020 08:18:42: 14000000 INFO @ Tue, 16 Jun 2020 08:18:45: 20000000 INFO @ Tue, 16 Jun 2020 08:18:45: 9000000 INFO @ Tue, 16 Jun 2020 08:18:48: 15000000 INFO @ Tue, 16 Jun 2020 08:18:50: 21000000 INFO @ Tue, 16 Jun 2020 08:18:51: 10000000 INFO @ Tue, 16 Jun 2020 08:18:53: 16000000 INFO @ Tue, 16 Jun 2020 08:18:56: 22000000 INFO @ Tue, 16 Jun 2020 08:18:56: 11000000 INFO @ Tue, 16 Jun 2020 08:18:59: 17000000 INFO @ Tue, 16 Jun 2020 08:19:00: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:19:00: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:19:00: #1 total tags in treatment: 22756571 INFO @ Tue, 16 Jun 2020 08:19:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:19:00: #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 08:19:01: #1 tags after filtering in treatment: 22756571 INFO @ Tue, 16 Jun 2020 08:19:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:19:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:19:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:19:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:19:02: 12000000 INFO @ Tue, 16 Jun 2020 08:19:02: #2 number of paired peaks: 195 WARNING @ Tue, 16 Jun 2020 08:19:02: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Tue, 16 Jun 2020 08:19:02: start model_add_line... INFO @ Tue, 16 Jun 2020 08:19:02: start X-correlation... INFO @ Tue, 16 Jun 2020 08:19:02: end of X-cor INFO @ Tue, 16 Jun 2020 08:19:02: #2 finished! INFO @ Tue, 16 Jun 2020 08:19:02: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:19:02: #2 alternative fragment length(s) may be 1,32,496,566 bps INFO @ Tue, 16 Jun 2020 08:19:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228898/SRX2228898.05_model.r WARNING @ Tue, 16 Jun 2020 08:19:02: #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 08:19:02: #2 You may need to consider one of the other alternative d(s): 1,32,496,566 WARNING @ Tue, 16 Jun 2020 08:19:02: #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 08:19:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:19:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:19:04: 18000000 INFO @ Tue, 16 Jun 2020 08:19:08: 13000000 INFO @ Tue, 16 Jun 2020 08:19:10: 19000000 INFO @ Tue, 16 Jun 2020 08:19:13: 14000000 INFO @ Tue, 16 Jun 2020 08:19:15: 20000000 INFO @ Tue, 16 Jun 2020 08:19:19: 15000000 INFO @ Tue, 16 Jun 2020 08:19:21: 21000000 INFO @ Tue, 16 Jun 2020 08:19:25: 16000000 INFO @ Tue, 16 Jun 2020 08:19:26: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:19:30: 17000000 INFO @ Tue, 16 Jun 2020 08:19:31: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:19:31: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:19:31: #1 total tags in treatment: 22756571 INFO @ Tue, 16 Jun 2020 08:19:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:19:31: #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 08:19:31: #1 tags after filtering in treatment: 22756571 INFO @ Tue, 16 Jun 2020 08:19:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:19:31: #1 finished! INFO @ Tue, 16 Jun 2020 08:19:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:19:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:19:33: #2 number of paired peaks: 195 WARNING @ Tue, 16 Jun 2020 08:19:33: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Tue, 16 Jun 2020 08:19:33: start model_add_line... INFO @ Tue, 16 Jun 2020 08:19:33: start X-correlation... INFO @ Tue, 16 Jun 2020 08:19:33: end of X-cor INFO @ Tue, 16 Jun 2020 08:19:33: #2 finished! INFO @ Tue, 16 Jun 2020 08:19:33: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:19:33: #2 alternative fragment length(s) may be 1,32,496,566 bps INFO @ Tue, 16 Jun 2020 08:19:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228898/SRX2228898.10_model.r WARNING @ Tue, 16 Jun 2020 08:19:33: #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 08:19:33: #2 You may need to consider one of the other alternative d(s): 1,32,496,566 WARNING @ Tue, 16 Jun 2020 08:19:33: #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 08:19:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:19:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:19:36: 18000000 INFO @ Tue, 16 Jun 2020 08:19:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:19:42: 19000000 INFO @ Tue, 16 Jun 2020 08:19:47: 20000000 INFO @ Tue, 16 Jun 2020 08:19:53: 21000000 INFO @ Tue, 16 Jun 2020 08:19:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228898/SRX2228898.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:19:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228898/SRX2228898.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:19:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228898/SRX2228898.05_summits.bed INFO @ Tue, 16 Jun 2020 08:19:55: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:19:58: 22000000 INFO @ Tue, 16 Jun 2020 08:20:03: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:20:03: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:20:03: #1 total tags in treatment: 22756571 INFO @ Tue, 16 Jun 2020 08:20:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:03: #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 08:20:03: #1 tags after filtering in treatment: 22756571 INFO @ Tue, 16 Jun 2020 08:20:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:20:03: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:05: #2 number of paired peaks: 195 WARNING @ Tue, 16 Jun 2020 08:20:05: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Tue, 16 Jun 2020 08:20:05: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:05: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:05: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:05: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:05: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:20:05: #2 alternative fragment length(s) may be 1,32,496,566 bps INFO @ Tue, 16 Jun 2020 08:20:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228898/SRX2228898.20_model.r WARNING @ Tue, 16 Jun 2020 08:20:05: #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 08:20:05: #2 You may need to consider one of the other alternative d(s): 1,32,496,566 WARNING @ Tue, 16 Jun 2020 08:20:05: #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 08:20:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:20:07: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:20:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228898/SRX2228898.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:20:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228898/SRX2228898.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:20:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228898/SRX2228898.10_summits.bed INFO @ Tue, 16 Jun 2020 08:20:24: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:20:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:20:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228898/SRX2228898.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:20:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228898/SRX2228898.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:20:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228898/SRX2228898.20_summits.bed INFO @ Tue, 16 Jun 2020 08:20:55: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling