Job ID = 6366055 SRX = SRX059227 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:36:36 prefetch.2.10.7: 1) Downloading 'SRR190667'... 2020-06-15T22:36:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:37:36 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:37:37 prefetch.2.10.7: 'SRR190667' is valid 2020-06-15T22:37:37 prefetch.2.10.7: 1) 'SRR190667' was downloaded successfully Read 16535439 spots for SRR190667/SRR190667.sra Written 16535439 spots for SRR190667/SRR190667.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:56 16535439 reads; of these: 16535439 (100.00%) were unpaired; of these: 460375 (2.78%) aligned 0 times 13205030 (79.86%) aligned exactly 1 time 2870034 (17.36%) aligned >1 times 97.22% overall alignment rate Time searching: 00:02:57 Overall time: 00:02:57 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_rmdupse_core] 1508338 / 16075064 = 0.0938 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 07:45:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059227/SRX059227.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059227/SRX059227.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059227/SRX059227.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059227/SRX059227.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 07:45:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:45:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:45:21: 1000000 INFO @ Tue, 16 Jun 2020 07:45:26: 2000000 INFO @ Tue, 16 Jun 2020 07:45:31: 3000000 INFO @ Tue, 16 Jun 2020 07:45:37: 4000000 INFO @ Tue, 16 Jun 2020 07:45:42: 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 07:45:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059227/SRX059227.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059227/SRX059227.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059227/SRX059227.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059227/SRX059227.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 07:45:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:45:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:45:48: 6000000 INFO @ Tue, 16 Jun 2020 07:45:52: 1000000 INFO @ Tue, 16 Jun 2020 07:45:54: 7000000 INFO @ Tue, 16 Jun 2020 07:45:58: 2000000 INFO @ Tue, 16 Jun 2020 07:46:00: 8000000 INFO @ Tue, 16 Jun 2020 07:46:05: 3000000 INFO @ Tue, 16 Jun 2020 07:46:06: 9000000 INFO @ Tue, 16 Jun 2020 07:46:11: 4000000 INFO @ Tue, 16 Jun 2020 07:46:12: 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 07:46:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059227/SRX059227.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059227/SRX059227.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059227/SRX059227.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059227/SRX059227.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 07:46:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:46:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:46:18: 11000000 INFO @ Tue, 16 Jun 2020 07:46:18: 5000000 INFO @ Tue, 16 Jun 2020 07:46:21: 1000000 INFO @ Tue, 16 Jun 2020 07:46:24: 12000000 INFO @ Tue, 16 Jun 2020 07:46:24: 6000000 INFO @ Tue, 16 Jun 2020 07:46:28: 2000000 INFO @ Tue, 16 Jun 2020 07:46:30: 13000000 INFO @ Tue, 16 Jun 2020 07:46:31: 7000000 INFO @ Tue, 16 Jun 2020 07:46:34: 3000000 INFO @ Tue, 16 Jun 2020 07:46:36: 14000000 INFO @ Tue, 16 Jun 2020 07:46:37: 8000000 INFO @ Tue, 16 Jun 2020 07:46:40: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:46:40: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:46:40: #1 total tags in treatment: 14566726 INFO @ Tue, 16 Jun 2020 07:46:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:46:40: #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 07:46:40: 4000000 INFO @ Tue, 16 Jun 2020 07:46:40: #1 tags after filtering in treatment: 14566726 INFO @ Tue, 16 Jun 2020 07:46:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:46:40: #1 finished! INFO @ Tue, 16 Jun 2020 07:46:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:46:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:46:41: #2 number of paired peaks: 268 WARNING @ Tue, 16 Jun 2020 07:46:41: Fewer paired peaks (268) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 268 pairs to build model! INFO @ Tue, 16 Jun 2020 07:46:41: start model_add_line... INFO @ Tue, 16 Jun 2020 07:46:41: start X-correlation... INFO @ Tue, 16 Jun 2020 07:46:41: end of X-cor INFO @ Tue, 16 Jun 2020 07:46:41: #2 finished! INFO @ Tue, 16 Jun 2020 07:46:41: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 07:46:41: #2 alternative fragment length(s) may be 1,21,35 bps INFO @ Tue, 16 Jun 2020 07:46:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059227/SRX059227.05_model.r WARNING @ Tue, 16 Jun 2020 07:46:41: #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 07:46:41: #2 You may need to consider one of the other alternative d(s): 1,21,35 WARNING @ Tue, 16 Jun 2020 07:46:41: #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 07:46:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:46:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:46:44: 9000000 INFO @ Tue, 16 Jun 2020 07:46:46: 5000000 INFO @ Tue, 16 Jun 2020 07:46:50: 10000000 INFO @ Tue, 16 Jun 2020 07:46:52: 6000000 INFO @ Tue, 16 Jun 2020 07:46:56: 11000000 INFO @ Tue, 16 Jun 2020 07:46:58: 7000000 INFO @ Tue, 16 Jun 2020 07:47:02: 12000000 INFO @ Tue, 16 Jun 2020 07:47:04: 8000000 INFO @ Tue, 16 Jun 2020 07:47:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:47:09: 13000000 INFO @ Tue, 16 Jun 2020 07:47:10: 9000000 INFO @ Tue, 16 Jun 2020 07:47:15: 14000000 INFO @ Tue, 16 Jun 2020 07:47:16: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:47:18: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:47:18: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:47:18: #1 total tags in treatment: 14566726 INFO @ Tue, 16 Jun 2020 07:47:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:47:18: #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 07:47:19: #1 tags after filtering in treatment: 14566726 INFO @ Tue, 16 Jun 2020 07:47:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:47:19: #1 finished! INFO @ Tue, 16 Jun 2020 07:47:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:47:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:47:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059227/SRX059227.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:47:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059227/SRX059227.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:47:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059227/SRX059227.05_summits.bed INFO @ Tue, 16 Jun 2020 07:47:20: Done! INFO @ Tue, 16 Jun 2020 07:47:20: #2 number of paired peaks: 268 WARNING @ Tue, 16 Jun 2020 07:47:20: Fewer paired peaks (268) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 268 pairs to build model! INFO @ Tue, 16 Jun 2020 07:47:20: start model_add_line... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:47:20: start X-correlation... INFO @ Tue, 16 Jun 2020 07:47:20: end of X-cor INFO @ Tue, 16 Jun 2020 07:47:20: #2 finished! INFO @ Tue, 16 Jun 2020 07:47:20: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 07:47:20: #2 alternative fragment length(s) may be 1,21,35 bps INFO @ Tue, 16 Jun 2020 07:47:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059227/SRX059227.10_model.r WARNING @ Tue, 16 Jun 2020 07:47:20: #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 07:47:20: #2 You may need to consider one of the other alternative d(s): 1,21,35 WARNING @ Tue, 16 Jun 2020 07:47:20: #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 07:47:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:47:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:47:22: 11000000 INFO @ Tue, 16 Jun 2020 07:47:28: 12000000 INFO @ Tue, 16 Jun 2020 07:47:33: 13000000 INFO @ Tue, 16 Jun 2020 07:47:39: 14000000 INFO @ Tue, 16 Jun 2020 07:47:42: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:47:42: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:47:42: #1 total tags in treatment: 14566726 INFO @ Tue, 16 Jun 2020 07:47:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:47:42: #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 07:47:42: #1 tags after filtering in treatment: 14566726 INFO @ Tue, 16 Jun 2020 07:47:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:47:42: #1 finished! INFO @ Tue, 16 Jun 2020 07:47:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:47:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:47:43: #2 number of paired peaks: 268 WARNING @ Tue, 16 Jun 2020 07:47:43: Fewer paired peaks (268) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 268 pairs to build model! INFO @ Tue, 16 Jun 2020 07:47:43: start model_add_line... INFO @ Tue, 16 Jun 2020 07:47:43: start X-correlation... INFO @ Tue, 16 Jun 2020 07:47:43: end of X-cor INFO @ Tue, 16 Jun 2020 07:47:43: #2 finished! INFO @ Tue, 16 Jun 2020 07:47:43: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 07:47:43: #2 alternative fragment length(s) may be 1,21,35 bps INFO @ Tue, 16 Jun 2020 07:47:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059227/SRX059227.20_model.r WARNING @ Tue, 16 Jun 2020 07:47:43: #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 07:47:43: #2 You may need to consider one of the other alternative d(s): 1,21,35 WARNING @ Tue, 16 Jun 2020 07:47:43: #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 07:47:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:47:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:47:43: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:47:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059227/SRX059227.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:47:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059227/SRX059227.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:47:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059227/SRX059227.10_summits.bed INFO @ Tue, 16 Jun 2020 07:47:55: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:48:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:48:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059227/SRX059227.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:48:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059227/SRX059227.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:48:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059227/SRX059227.20_summits.bed INFO @ Tue, 16 Jun 2020 07:48:20: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling