Job ID = 6366821 SRX = SRX2350720 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 'SRR5024029'... 2020-06-15T23:14:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:15:44 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:15:44 prefetch.2.10.7: 1) 'SRR5024029' was downloaded successfully Read 14168528 spots for SRR5024029/SRR5024029.sra Written 14168528 spots for SRR5024029/SRR5024029.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: 00:03:39 14168528 reads; of these: 14168528 (100.00%) were unpaired; of these: 435307 (3.07%) aligned 0 times 10161174 (71.72%) aligned exactly 1 time 3572047 (25.21%) aligned >1 times 96.93% overall alignment rate Time searching: 00:03:39 Overall time: 00:03:39 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] 2435009 / 13733221 = 0.1773 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 08:23:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350720/SRX2350720.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350720/SRX2350720.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350720/SRX2350720.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350720/SRX2350720.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 08:23:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:23:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:04: 1000000 INFO @ Tue, 16 Jun 2020 08:24:10: 2000000 INFO @ Tue, 16 Jun 2020 08:24:17: 3000000 INFO @ Tue, 16 Jun 2020 08:24:23: 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 08:24:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350720/SRX2350720.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350720/SRX2350720.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350720/SRX2350720.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350720/SRX2350720.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 08:24:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:24:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:29: 5000000 INFO @ Tue, 16 Jun 2020 08:24:35: 1000000 INFO @ Tue, 16 Jun 2020 08:24:36: 6000000 INFO @ Tue, 16 Jun 2020 08:24:41: 2000000 INFO @ Tue, 16 Jun 2020 08:24:43: 7000000 INFO @ Tue, 16 Jun 2020 08:24:48: 3000000 INFO @ Tue, 16 Jun 2020 08:24:50: 8000000 INFO @ Tue, 16 Jun 2020 08:24:55: 4000000 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 08:24:58: 9000000 INFO @ Tue, 16 Jun 2020 08:24:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350720/SRX2350720.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350720/SRX2350720.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350720/SRX2350720.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350720/SRX2350720.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 08:24:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:24:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:02: 5000000 INFO @ Tue, 16 Jun 2020 08:25:05: 1000000 INFO @ Tue, 16 Jun 2020 08:25:05: 10000000 INFO @ Tue, 16 Jun 2020 08:25:09: 6000000 INFO @ Tue, 16 Jun 2020 08:25:12: 2000000 INFO @ Tue, 16 Jun 2020 08:25:12: 11000000 INFO @ Tue, 16 Jun 2020 08:25:14: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:25:14: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:25:14: #1 total tags in treatment: 11298212 INFO @ Tue, 16 Jun 2020 08:25:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:25:14: #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 08:25:14: #1 tags after filtering in treatment: 11298212 INFO @ Tue, 16 Jun 2020 08:25:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:25:14: #1 finished! INFO @ Tue, 16 Jun 2020 08:25:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:25:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:25:15: #2 number of paired peaks: 509 WARNING @ Tue, 16 Jun 2020 08:25:15: Fewer paired peaks (509) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 509 pairs to build model! INFO @ Tue, 16 Jun 2020 08:25:15: start model_add_line... INFO @ Tue, 16 Jun 2020 08:25:15: start X-correlation... INFO @ Tue, 16 Jun 2020 08:25:15: end of X-cor INFO @ Tue, 16 Jun 2020 08:25:15: #2 finished! INFO @ Tue, 16 Jun 2020 08:25:15: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 08:25:15: #2 alternative fragment length(s) may be 2,31,45 bps INFO @ Tue, 16 Jun 2020 08:25:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350720/SRX2350720.05_model.r WARNING @ Tue, 16 Jun 2020 08:25:15: #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 08:25:15: #2 You may need to consider one of the other alternative d(s): 2,31,45 WARNING @ Tue, 16 Jun 2020 08:25:15: #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 08:25:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:25:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:25:16: 7000000 INFO @ Tue, 16 Jun 2020 08:25:19: 3000000 INFO @ Tue, 16 Jun 2020 08:25:23: 8000000 INFO @ Tue, 16 Jun 2020 08:25:26: 4000000 INFO @ Tue, 16 Jun 2020 08:25:31: 9000000 INFO @ Tue, 16 Jun 2020 08:25:33: 5000000 INFO @ Tue, 16 Jun 2020 08:25:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:25:38: 10000000 INFO @ Tue, 16 Jun 2020 08:25:40: 6000000 INFO @ Tue, 16 Jun 2020 08:25:45: 11000000 INFO @ Tue, 16 Jun 2020 08:25:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350720/SRX2350720.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:25:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350720/SRX2350720.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:25:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350720/SRX2350720.05_summits.bed INFO @ Tue, 16 Jun 2020 08:25:47: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:25:47: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:25:47: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:25:47: #1 total tags in treatment: 11298212 INFO @ Tue, 16 Jun 2020 08:25:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:25:47: #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 08:25:47: #1 tags after filtering in treatment: 11298212 INFO @ Tue, 16 Jun 2020 08:25:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:25:47: #1 finished! INFO @ Tue, 16 Jun 2020 08:25:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:25:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:25:47: 7000000 INFO @ Tue, 16 Jun 2020 08:25:48: #2 number of paired peaks: 509 WARNING @ Tue, 16 Jun 2020 08:25:48: Fewer paired peaks (509) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 509 pairs to build model! INFO @ Tue, 16 Jun 2020 08:25:48: start model_add_line... INFO @ Tue, 16 Jun 2020 08:25:48: start X-correlation... INFO @ Tue, 16 Jun 2020 08:25:48: end of X-cor INFO @ Tue, 16 Jun 2020 08:25:48: #2 finished! INFO @ Tue, 16 Jun 2020 08:25:48: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 08:25:48: #2 alternative fragment length(s) may be 2,31,45 bps INFO @ Tue, 16 Jun 2020 08:25:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350720/SRX2350720.10_model.r WARNING @ Tue, 16 Jun 2020 08:25:48: #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 08:25:48: #2 You may need to consider one of the other alternative d(s): 2,31,45 WARNING @ Tue, 16 Jun 2020 08:25:48: #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 08:25:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:25:48: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:25:54: 8000000 INFO @ Tue, 16 Jun 2020 08:26:00: 9000000 INFO @ Tue, 16 Jun 2020 08:26:07: 10000000 INFO @ Tue, 16 Jun 2020 08:26:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:26:13: 11000000 INFO @ Tue, 16 Jun 2020 08:26:15: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:26:15: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:26:15: #1 total tags in treatment: 11298212 INFO @ Tue, 16 Jun 2020 08:26:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:15: #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 08:26:15: #1 tags after filtering in treatment: 11298212 INFO @ Tue, 16 Jun 2020 08:26:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:15: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:16: #2 number of paired peaks: 509 WARNING @ Tue, 16 Jun 2020 08:26:16: Fewer paired peaks (509) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 509 pairs to build model! INFO @ Tue, 16 Jun 2020 08:26:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:16: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:16: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:16: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:16: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 08:26:16: #2 alternative fragment length(s) may be 2,31,45 bps INFO @ Tue, 16 Jun 2020 08:26:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350720/SRX2350720.20_model.r WARNING @ Tue, 16 Jun 2020 08:26:16: #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 08:26:16: #2 You may need to consider one of the other alternative d(s): 2,31,45 WARNING @ Tue, 16 Jun 2020 08:26:16: #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 08:26:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:26:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350720/SRX2350720.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:26:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350720/SRX2350720.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:26:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350720/SRX2350720.10_summits.bed INFO @ Tue, 16 Jun 2020 08:26:19: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:26:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:26:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350720/SRX2350720.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:26:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350720/SRX2350720.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:26:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350720/SRX2350720.20_summits.bed INFO @ Tue, 16 Jun 2020 08:26:47: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling