Job ID = 6366871 SRX = SRX245914 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 'SRR765971'... 2020-06-15T23:03:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:05:22 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:05:22 prefetch.2.10.7: 1) 'SRR765971' was downloaded successfully Read 21734004 spots for SRR765971/SRR765971.sra Written 21734004 spots for SRR765971/SRR765971.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: 00:03:44 21734004 reads; of these: 21734004 (100.00%) were unpaired; of these: 1831829 (8.43%) aligned 0 times 16569827 (76.24%) aligned exactly 1 time 3332348 (15.33%) aligned >1 times 91.57% overall alignment rate Time searching: 00:03:44 Overall time: 00:03:44 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] 1647435 / 19902175 = 0.0828 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 08:14:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX245914/SRX245914.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX245914/SRX245914.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX245914/SRX245914.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX245914/SRX245914.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 08:14:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:45: 1000000 INFO @ Tue, 16 Jun 2020 08:14:51: 2000000 INFO @ Tue, 16 Jun 2020 08:14:57: 3000000 INFO @ Tue, 16 Jun 2020 08:15:03: 4000000 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 08:15:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX245914/SRX245914.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX245914/SRX245914.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX245914/SRX245914.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX245914/SRX245914.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 08:15:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:09: 5000000 INFO @ Tue, 16 Jun 2020 08:15:15: 1000000 INFO @ Tue, 16 Jun 2020 08:15:16: 6000000 INFO @ Tue, 16 Jun 2020 08:15:22: 2000000 INFO @ Tue, 16 Jun 2020 08:15:22: 7000000 INFO @ Tue, 16 Jun 2020 08:15:29: 3000000 INFO @ Tue, 16 Jun 2020 08:15:29: 8000000 INFO @ Tue, 16 Jun 2020 08:15:35: 4000000 INFO @ Tue, 16 Jun 2020 08:15:35: 9000000 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 08:15:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX245914/SRX245914.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX245914/SRX245914.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX245914/SRX245914.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX245914/SRX245914.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 08:15:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:42: 10000000 INFO @ Tue, 16 Jun 2020 08:15:42: 5000000 INFO @ Tue, 16 Jun 2020 08:15:45: 1000000 INFO @ Tue, 16 Jun 2020 08:15:48: 11000000 INFO @ Tue, 16 Jun 2020 08:15:48: 6000000 INFO @ Tue, 16 Jun 2020 08:15:52: 2000000 INFO @ Tue, 16 Jun 2020 08:15:55: 12000000 INFO @ Tue, 16 Jun 2020 08:15:55: 7000000 INFO @ Tue, 16 Jun 2020 08:15:58: 3000000 INFO @ Tue, 16 Jun 2020 08:16:01: 13000000 INFO @ Tue, 16 Jun 2020 08:16:02: 8000000 INFO @ Tue, 16 Jun 2020 08:16:05: 4000000 INFO @ Tue, 16 Jun 2020 08:16:08: 14000000 INFO @ Tue, 16 Jun 2020 08:16:08: 9000000 INFO @ Tue, 16 Jun 2020 08:16:12: 5000000 INFO @ Tue, 16 Jun 2020 08:16:14: 15000000 INFO @ Tue, 16 Jun 2020 08:16:15: 10000000 INFO @ Tue, 16 Jun 2020 08:16:18: 6000000 INFO @ Tue, 16 Jun 2020 08:16:21: 16000000 INFO @ Tue, 16 Jun 2020 08:16:21: 11000000 INFO @ Tue, 16 Jun 2020 08:16:25: 7000000 INFO @ Tue, 16 Jun 2020 08:16:27: 17000000 INFO @ Tue, 16 Jun 2020 08:16:28: 12000000 INFO @ Tue, 16 Jun 2020 08:16:31: 8000000 INFO @ Tue, 16 Jun 2020 08:16:34: 18000000 INFO @ Tue, 16 Jun 2020 08:16:34: 13000000 INFO @ Tue, 16 Jun 2020 08:16:36: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:16:36: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:16:36: #1 total tags in treatment: 18254740 INFO @ Tue, 16 Jun 2020 08:16:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:16:36: #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 08:16:36: #1 tags after filtering in treatment: 18254740 INFO @ Tue, 16 Jun 2020 08:16:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:16:36: #1 finished! INFO @ Tue, 16 Jun 2020 08:16:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:16:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:16:37: #2 number of paired peaks: 225 WARNING @ Tue, 16 Jun 2020 08:16:37: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Tue, 16 Jun 2020 08:16:37: start model_add_line... INFO @ Tue, 16 Jun 2020 08:16:37: start X-correlation... INFO @ Tue, 16 Jun 2020 08:16:37: end of X-cor INFO @ Tue, 16 Jun 2020 08:16:37: #2 finished! INFO @ Tue, 16 Jun 2020 08:16:37: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:16:37: #2 alternative fragment length(s) may be 1,33,146,490,511,529 bps INFO @ Tue, 16 Jun 2020 08:16:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX245914/SRX245914.05_model.r WARNING @ Tue, 16 Jun 2020 08:16:37: #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 08:16:37: #2 You may need to consider one of the other alternative d(s): 1,33,146,490,511,529 WARNING @ Tue, 16 Jun 2020 08:16:37: #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 08:16:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:16:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:16:38: 9000000 INFO @ Tue, 16 Jun 2020 08:16:41: 14000000 INFO @ Tue, 16 Jun 2020 08:16:44: 10000000 INFO @ Tue, 16 Jun 2020 08:16:47: 15000000 INFO @ Tue, 16 Jun 2020 08:16:50: 11000000 INFO @ Tue, 16 Jun 2020 08:16:54: 16000000 INFO @ Tue, 16 Jun 2020 08:16:57: 12000000 INFO @ Tue, 16 Jun 2020 08:17:00: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:17:03: 13000000 INFO @ Tue, 16 Jun 2020 08:17:07: 18000000 INFO @ Tue, 16 Jun 2020 08:17:08: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:17:08: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:17:08: #1 total tags in treatment: 18254740 INFO @ Tue, 16 Jun 2020 08:17:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:17:08: #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 08:17:09: #1 tags after filtering in treatment: 18254740 INFO @ Tue, 16 Jun 2020 08:17:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:17:09: #1 finished! INFO @ Tue, 16 Jun 2020 08:17:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:17:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:17:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:17:09: 14000000 INFO @ Tue, 16 Jun 2020 08:17:10: #2 number of paired peaks: 225 WARNING @ Tue, 16 Jun 2020 08:17:10: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Tue, 16 Jun 2020 08:17:10: start model_add_line... INFO @ Tue, 16 Jun 2020 08:17:10: start X-correlation... INFO @ Tue, 16 Jun 2020 08:17:10: end of X-cor INFO @ Tue, 16 Jun 2020 08:17:10: #2 finished! INFO @ Tue, 16 Jun 2020 08:17:10: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:17:10: #2 alternative fragment length(s) may be 1,33,146,490,511,529 bps INFO @ Tue, 16 Jun 2020 08:17:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX245914/SRX245914.10_model.r WARNING @ Tue, 16 Jun 2020 08:17:10: #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 08:17:10: #2 You may need to consider one of the other alternative d(s): 1,33,146,490,511,529 WARNING @ Tue, 16 Jun 2020 08:17:10: #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 08:17:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:17:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:17:16: 15000000 INFO @ Tue, 16 Jun 2020 08:17:21: 16000000 INFO @ Tue, 16 Jun 2020 08:17:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX245914/SRX245914.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:17:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX245914/SRX245914.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:17:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX245914/SRX245914.05_summits.bed INFO @ Tue, 16 Jun 2020 08:17:25: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:17:27: 17000000 INFO @ Tue, 16 Jun 2020 08:17:33: 18000000 INFO @ Tue, 16 Jun 2020 08:17:35: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:17:35: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:17:35: #1 total tags in treatment: 18254740 INFO @ Tue, 16 Jun 2020 08:17:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:17:35: #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 08:17:35: #1 tags after filtering in treatment: 18254740 INFO @ Tue, 16 Jun 2020 08:17:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:17:35: #1 finished! INFO @ Tue, 16 Jun 2020 08:17:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:17:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:17:36: #2 number of paired peaks: 225 WARNING @ Tue, 16 Jun 2020 08:17:36: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Tue, 16 Jun 2020 08:17:36: start model_add_line... INFO @ Tue, 16 Jun 2020 08:17:36: start X-correlation... INFO @ Tue, 16 Jun 2020 08:17:36: end of X-cor INFO @ Tue, 16 Jun 2020 08:17:36: #2 finished! INFO @ Tue, 16 Jun 2020 08:17:36: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:17:36: #2 alternative fragment length(s) may be 1,33,146,490,511,529 bps INFO @ Tue, 16 Jun 2020 08:17:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX245914/SRX245914.20_model.r WARNING @ Tue, 16 Jun 2020 08:17:36: #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 08:17:36: #2 You may need to consider one of the other alternative d(s): 1,33,146,490,511,529 WARNING @ Tue, 16 Jun 2020 08:17:36: #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 08:17:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:17:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:17:41: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:17:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX245914/SRX245914.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:17:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX245914/SRX245914.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:17:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX245914/SRX245914.10_summits.bed INFO @ Tue, 16 Jun 2020 08:17:57: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:18:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:18:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX245914/SRX245914.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:18:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX245914/SRX245914.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:18:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX245914/SRX245914.20_summits.bed INFO @ Tue, 16 Jun 2020 08:18:22: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling