Job ID = 6507857 SRX = SRX494940 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:53:57 prefetch.2.10.7: 1) Downloading 'SRR1198472'... 2020-06-26T13:53:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:56:09 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:56:09 prefetch.2.10.7: 1) 'SRR1198472' was downloaded successfully Read 24434363 spots for SRR1198472/SRR1198472.sra Written 24434363 spots for SRR1198472/SRR1198472.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: 00:00:01 Multiseed full-index search: 00:05:31 24434363 reads; of these: 24434363 (100.00%) were unpaired; of these: 3204874 (13.12%) aligned 0 times 17393156 (71.18%) aligned exactly 1 time 3836333 (15.70%) aligned >1 times 86.88% overall alignment rate Time searching: 00:05:32 Overall time: 00:05:32 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 12 files... [bam_rmdupse_core] 2473110 / 21229489 = 0.1165 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 @ Fri, 26 Jun 2020 23:08:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494940/SRX494940.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494940/SRX494940.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494940/SRX494940.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494940/SRX494940.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 @ Fri, 26 Jun 2020 23:08:41: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:08:41: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:08:47: 1000000 INFO @ Fri, 26 Jun 2020 23:08:52: 2000000 INFO @ Fri, 26 Jun 2020 23:08:58: 3000000 INFO @ Fri, 26 Jun 2020 23:09:04: 4000000 INFO @ Fri, 26 Jun 2020 23:09:09: 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 @ Fri, 26 Jun 2020 23:09:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494940/SRX494940.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494940/SRX494940.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494940/SRX494940.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494940/SRX494940.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 @ Fri, 26 Jun 2020 23:09:11: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:09:11: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:09:15: 6000000 INFO @ Fri, 26 Jun 2020 23:09:17: 1000000 INFO @ Fri, 26 Jun 2020 23:09:21: 7000000 INFO @ Fri, 26 Jun 2020 23:09:23: 2000000 INFO @ Fri, 26 Jun 2020 23:09:27: 8000000 INFO @ Fri, 26 Jun 2020 23:09:29: 3000000 INFO @ Fri, 26 Jun 2020 23:09:33: 9000000 INFO @ Fri, 26 Jun 2020 23:09:35: 4000000 INFO @ Fri, 26 Jun 2020 23:09:39: 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 @ Fri, 26 Jun 2020 23:09:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494940/SRX494940.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494940/SRX494940.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494940/SRX494940.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494940/SRX494940.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 @ Fri, 26 Jun 2020 23:09:41: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:09:41: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:09:42: 5000000 INFO @ Fri, 26 Jun 2020 23:09:45: 11000000 INFO @ Fri, 26 Jun 2020 23:09:47: 1000000 INFO @ Fri, 26 Jun 2020 23:09:48: 6000000 INFO @ Fri, 26 Jun 2020 23:09:51: 12000000 INFO @ Fri, 26 Jun 2020 23:09:53: 2000000 INFO @ Fri, 26 Jun 2020 23:09:55: 7000000 INFO @ Fri, 26 Jun 2020 23:09:56: 13000000 INFO @ Fri, 26 Jun 2020 23:10:00: 3000000 INFO @ Fri, 26 Jun 2020 23:10:02: 8000000 INFO @ Fri, 26 Jun 2020 23:10:03: 14000000 INFO @ Fri, 26 Jun 2020 23:10:06: 4000000 INFO @ Fri, 26 Jun 2020 23:10:08: 15000000 INFO @ Fri, 26 Jun 2020 23:10:09: 9000000 INFO @ Fri, 26 Jun 2020 23:10:12: 5000000 INFO @ Fri, 26 Jun 2020 23:10:14: 16000000 INFO @ Fri, 26 Jun 2020 23:10:16: 10000000 INFO @ Fri, 26 Jun 2020 23:10:19: 6000000 INFO @ Fri, 26 Jun 2020 23:10:20: 17000000 INFO @ Fri, 26 Jun 2020 23:10:23: 11000000 INFO @ Fri, 26 Jun 2020 23:10:26: 7000000 INFO @ Fri, 26 Jun 2020 23:10:26: 18000000 INFO @ Fri, 26 Jun 2020 23:10:29: 12000000 INFO @ Fri, 26 Jun 2020 23:10:31: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:10:31: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:10:31: #1 total tags in treatment: 18756379 INFO @ Fri, 26 Jun 2020 23:10:31: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:10:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:10:31: #1 tags after filtering in treatment: 18756379 INFO @ Fri, 26 Jun 2020 23:10:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:10:31: #1 finished! INFO @ Fri, 26 Jun 2020 23:10:31: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:10:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:10:33: #2 number of paired peaks: 240 WARNING @ Fri, 26 Jun 2020 23:10:33: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Fri, 26 Jun 2020 23:10:33: start model_add_line... INFO @ Fri, 26 Jun 2020 23:10:33: 8000000 INFO @ Fri, 26 Jun 2020 23:10:33: start X-correlation... INFO @ Fri, 26 Jun 2020 23:10:33: end of X-cor INFO @ Fri, 26 Jun 2020 23:10:33: #2 finished! INFO @ Fri, 26 Jun 2020 23:10:33: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:10:33: #2 alternative fragment length(s) may be 1,11,33,536,589 bps INFO @ Fri, 26 Jun 2020 23:10:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494940/SRX494940.05_model.r WARNING @ Fri, 26 Jun 2020 23:10:33: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:10:33: #2 You may need to consider one of the other alternative d(s): 1,11,33,536,589 WARNING @ Fri, 26 Jun 2020 23:10:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:10:33: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:10:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:10:36: 13000000 INFO @ Fri, 26 Jun 2020 23:10:40: 9000000 INFO @ Fri, 26 Jun 2020 23:10:42: 14000000 INFO @ Fri, 26 Jun 2020 23:10:46: 10000000 INFO @ Fri, 26 Jun 2020 23:10:48: 15000000 INFO @ Fri, 26 Jun 2020 23:10:52: 11000000 INFO @ Fri, 26 Jun 2020 23:10:54: 16000000 INFO @ Fri, 26 Jun 2020 23:10:59: 12000000 INFO @ Fri, 26 Jun 2020 23:11:00: 17000000 INFO @ Fri, 26 Jun 2020 23:11:05: 13000000 INFO @ Fri, 26 Jun 2020 23:11:06: 18000000 INFO @ Fri, 26 Jun 2020 23:11:07: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:11:10: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:11:10: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:11:10: #1 total tags in treatment: 18756379 INFO @ Fri, 26 Jun 2020 23:11:10: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:11:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:11:11: #1 tags after filtering in treatment: 18756379 INFO @ Fri, 26 Jun 2020 23:11:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:11:11: #1 finished! INFO @ Fri, 26 Jun 2020 23:11:11: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:11:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:11:11: 14000000 INFO @ Fri, 26 Jun 2020 23:11:12: #2 number of paired peaks: 240 WARNING @ Fri, 26 Jun 2020 23:11:12: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Fri, 26 Jun 2020 23:11:12: start model_add_line... INFO @ Fri, 26 Jun 2020 23:11:12: start X-correlation... INFO @ Fri, 26 Jun 2020 23:11:12: end of X-cor INFO @ Fri, 26 Jun 2020 23:11:12: #2 finished! INFO @ Fri, 26 Jun 2020 23:11:12: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:11:12: #2 alternative fragment length(s) may be 1,11,33,536,589 bps INFO @ Fri, 26 Jun 2020 23:11:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494940/SRX494940.10_model.r WARNING @ Fri, 26 Jun 2020 23:11:12: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:11:12: #2 You may need to consider one of the other alternative d(s): 1,11,33,536,589 WARNING @ Fri, 26 Jun 2020 23:11:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:11:12: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:11:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:11:17: 15000000 INFO @ Fri, 26 Jun 2020 23:11:23: 16000000 INFO @ Fri, 26 Jun 2020 23:11:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494940/SRX494940.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:11:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494940/SRX494940.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:11:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494940/SRX494940.05_summits.bed INFO @ Fri, 26 Jun 2020 23:11:23: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:11:28: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:11:34: 18000000 INFO @ Fri, 26 Jun 2020 23:11:38: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:11:38: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:11:38: #1 total tags in treatment: 18756379 INFO @ Fri, 26 Jun 2020 23:11:38: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:11:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:11:38: #1 tags after filtering in treatment: 18756379 INFO @ Fri, 26 Jun 2020 23:11:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:11:38: #1 finished! INFO @ Fri, 26 Jun 2020 23:11:38: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:11:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:11:40: #2 number of paired peaks: 240 WARNING @ Fri, 26 Jun 2020 23:11:40: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Fri, 26 Jun 2020 23:11:40: start model_add_line... INFO @ Fri, 26 Jun 2020 23:11:40: start X-correlation... INFO @ Fri, 26 Jun 2020 23:11:40: end of X-cor INFO @ Fri, 26 Jun 2020 23:11:40: #2 finished! INFO @ Fri, 26 Jun 2020 23:11:40: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:11:40: #2 alternative fragment length(s) may be 1,11,33,536,589 bps INFO @ Fri, 26 Jun 2020 23:11:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494940/SRX494940.20_model.r WARNING @ Fri, 26 Jun 2020 23:11:40: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:11:40: #2 You may need to consider one of the other alternative d(s): 1,11,33,536,589 WARNING @ Fri, 26 Jun 2020 23:11:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:11:40: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:11:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:11:47: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:12:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494940/SRX494940.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:12:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494940/SRX494940.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:12:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494940/SRX494940.10_summits.bed INFO @ Fri, 26 Jun 2020 23:12:03: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:12:13: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:12:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494940/SRX494940.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:12:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494940/SRX494940.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:12:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494940/SRX494940.20_summits.bed INFO @ Fri, 26 Jun 2020 23:12:29: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling