Job ID = 6497447 SRX = SRX494945 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:32:04 prefetch.2.10.7: 1) Downloading 'SRR1198477'... 2020-06-25T22:32:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:37:42 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:37:42 prefetch.2.10.7: 1) 'SRR1198477' was downloaded successfully Read 27753616 spots for SRR1198477/SRR1198477.sra Written 27753616 spots for SRR1198477/SRR1198477.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: 00:06:35 27753616 reads; of these: 27753616 (100.00%) were unpaired; of these: 2485219 (8.95%) aligned 0 times 20590606 (74.19%) aligned exactly 1 time 4677791 (16.85%) aligned >1 times 91.05% overall alignment rate Time searching: 00:06:35 Overall time: 00:06:35 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] 5161883 / 25268397 = 0.2043 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 07:52:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494945/SRX494945.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494945/SRX494945.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494945/SRX494945.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494945/SRX494945.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 07:52:14: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:52:14: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:52:21: 1000000 INFO @ Fri, 26 Jun 2020 07:52:27: 2000000 INFO @ Fri, 26 Jun 2020 07:52:34: 3000000 INFO @ Fri, 26 Jun 2020 07:52:41: 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 @ Fri, 26 Jun 2020 07:52:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494945/SRX494945.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494945/SRX494945.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494945/SRX494945.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494945/SRX494945.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 07:52:44: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:52:44: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:52:48: 5000000 INFO @ Fri, 26 Jun 2020 07:52:51: 1000000 INFO @ Fri, 26 Jun 2020 07:52:55: 6000000 INFO @ Fri, 26 Jun 2020 07:52:59: 2000000 INFO @ Fri, 26 Jun 2020 07:53:03: 7000000 INFO @ Fri, 26 Jun 2020 07:53:06: 3000000 INFO @ Fri, 26 Jun 2020 07:53:10: 8000000 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 07:53:13: 4000000 INFO @ Fri, 26 Jun 2020 07:53:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494945/SRX494945.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494945/SRX494945.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494945/SRX494945.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494945/SRX494945.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 07:53:14: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:53:14: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:53:18: 9000000 INFO @ Fri, 26 Jun 2020 07:53:21: 5000000 INFO @ Fri, 26 Jun 2020 07:53:21: 1000000 INFO @ Fri, 26 Jun 2020 07:53:25: 10000000 INFO @ Fri, 26 Jun 2020 07:53:28: 6000000 INFO @ Fri, 26 Jun 2020 07:53:29: 2000000 INFO @ Fri, 26 Jun 2020 07:53:33: 11000000 INFO @ Fri, 26 Jun 2020 07:53:36: 7000000 INFO @ Fri, 26 Jun 2020 07:53:36: 3000000 INFO @ Fri, 26 Jun 2020 07:53:40: 12000000 INFO @ Fri, 26 Jun 2020 07:53:43: 8000000 INFO @ Fri, 26 Jun 2020 07:53:44: 4000000 INFO @ Fri, 26 Jun 2020 07:53:48: 13000000 INFO @ Fri, 26 Jun 2020 07:53:51: 9000000 INFO @ Fri, 26 Jun 2020 07:53:51: 5000000 INFO @ Fri, 26 Jun 2020 07:53:55: 14000000 INFO @ Fri, 26 Jun 2020 07:53:58: 10000000 INFO @ Fri, 26 Jun 2020 07:53:59: 6000000 INFO @ Fri, 26 Jun 2020 07:54:03: 15000000 INFO @ Fri, 26 Jun 2020 07:54:06: 11000000 INFO @ Fri, 26 Jun 2020 07:54:06: 7000000 INFO @ Fri, 26 Jun 2020 07:54:10: 16000000 INFO @ Fri, 26 Jun 2020 07:54:13: 12000000 INFO @ Fri, 26 Jun 2020 07:54:14: 8000000 INFO @ Fri, 26 Jun 2020 07:54:18: 17000000 INFO @ Fri, 26 Jun 2020 07:54:20: 13000000 INFO @ Fri, 26 Jun 2020 07:54:21: 9000000 INFO @ Fri, 26 Jun 2020 07:54:25: 18000000 INFO @ Fri, 26 Jun 2020 07:54:28: 14000000 INFO @ Fri, 26 Jun 2020 07:54:29: 10000000 INFO @ Fri, 26 Jun 2020 07:54:33: 19000000 INFO @ Fri, 26 Jun 2020 07:54:35: 15000000 INFO @ Fri, 26 Jun 2020 07:54:36: 11000000 INFO @ Fri, 26 Jun 2020 07:54:40: 20000000 INFO @ Fri, 26 Jun 2020 07:54:41: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:54:41: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:54:41: #1 total tags in treatment: 20106514 INFO @ Fri, 26 Jun 2020 07:54:41: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:54:41: #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 07:54:41: #1 tags after filtering in treatment: 20106514 INFO @ Fri, 26 Jun 2020 07:54:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:54:41: #1 finished! INFO @ Fri, 26 Jun 2020 07:54:41: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:54:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:54:43: 16000000 INFO @ Fri, 26 Jun 2020 07:54:43: #2 number of paired peaks: 226 WARNING @ Fri, 26 Jun 2020 07:54:43: Fewer paired peaks (226) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 226 pairs to build model! INFO @ Fri, 26 Jun 2020 07:54:43: start model_add_line... INFO @ Fri, 26 Jun 2020 07:54:43: start X-correlation... INFO @ Fri, 26 Jun 2020 07:54:43: end of X-cor INFO @ Fri, 26 Jun 2020 07:54:43: #2 finished! INFO @ Fri, 26 Jun 2020 07:54:43: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:54:43: #2 alternative fragment length(s) may be 1,32,47,567,589 bps INFO @ Fri, 26 Jun 2020 07:54:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494945/SRX494945.05_model.r WARNING @ Fri, 26 Jun 2020 07:54:43: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:54:43: #2 You may need to consider one of the other alternative d(s): 1,32,47,567,589 WARNING @ Fri, 26 Jun 2020 07:54:43: #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 07:54:43: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:54:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:54:44: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:54:50: 17000000 INFO @ Fri, 26 Jun 2020 07:54:51: 13000000 INFO @ Fri, 26 Jun 2020 07:54:57: 18000000 INFO @ Fri, 26 Jun 2020 07:54:58: 14000000 INFO @ Fri, 26 Jun 2020 07:55:04: 19000000 INFO @ Fri, 26 Jun 2020 07:55:05: 15000000 INFO @ Fri, 26 Jun 2020 07:55:12: 20000000 INFO @ Fri, 26 Jun 2020 07:55:12: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:55:12: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:55:12: #1 total tags in treatment: 20106514 INFO @ Fri, 26 Jun 2020 07:55:12: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:55:12: #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 07:55:12: 16000000 INFO @ Fri, 26 Jun 2020 07:55:13: #1 tags after filtering in treatment: 20106514 INFO @ Fri, 26 Jun 2020 07:55:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:55:13: #1 finished! INFO @ Fri, 26 Jun 2020 07:55:13: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:55:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:55:14: #2 number of paired peaks: 226 WARNING @ Fri, 26 Jun 2020 07:55:14: Fewer paired peaks (226) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 226 pairs to build model! INFO @ Fri, 26 Jun 2020 07:55:14: start model_add_line... INFO @ Fri, 26 Jun 2020 07:55:14: start X-correlation... INFO @ Fri, 26 Jun 2020 07:55:14: end of X-cor INFO @ Fri, 26 Jun 2020 07:55:14: #2 finished! INFO @ Fri, 26 Jun 2020 07:55:14: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:55:14: #2 alternative fragment length(s) may be 1,32,47,567,589 bps INFO @ Fri, 26 Jun 2020 07:55:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494945/SRX494945.10_model.r WARNING @ Fri, 26 Jun 2020 07:55:14: #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 07:55:14: #2 You may need to consider one of the other alternative d(s): 1,32,47,567,589 WARNING @ Fri, 26 Jun 2020 07:55:14: #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 07:55:14: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:55:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:55:18: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:55:19: 17000000 INFO @ Fri, 26 Jun 2020 07:55:25: 18000000 INFO @ Fri, 26 Jun 2020 07:55:32: 19000000 INFO @ Fri, 26 Jun 2020 07:55:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494945/SRX494945.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:55:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494945/SRX494945.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:55:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494945/SRX494945.05_summits.bed INFO @ Fri, 26 Jun 2020 07:55:33: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:55:38: 20000000 INFO @ Fri, 26 Jun 2020 07:55:39: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:55:39: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:55:39: #1 total tags in treatment: 20106514 INFO @ Fri, 26 Jun 2020 07:55:39: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:55:39: #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 07:55:40: #1 tags after filtering in treatment: 20106514 INFO @ Fri, 26 Jun 2020 07:55:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:55:40: #1 finished! INFO @ Fri, 26 Jun 2020 07:55:40: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:55:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:55:41: #2 number of paired peaks: 226 WARNING @ Fri, 26 Jun 2020 07:55:41: Fewer paired peaks (226) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 226 pairs to build model! INFO @ Fri, 26 Jun 2020 07:55:41: start model_add_line... INFO @ Fri, 26 Jun 2020 07:55:41: start X-correlation... INFO @ Fri, 26 Jun 2020 07:55:41: end of X-cor INFO @ Fri, 26 Jun 2020 07:55:41: #2 finished! INFO @ Fri, 26 Jun 2020 07:55:41: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:55:41: #2 alternative fragment length(s) may be 1,32,47,567,589 bps INFO @ Fri, 26 Jun 2020 07:55:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494945/SRX494945.20_model.r WARNING @ Fri, 26 Jun 2020 07:55:41: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:55:41: #2 You may need to consider one of the other alternative d(s): 1,32,47,567,589 WARNING @ Fri, 26 Jun 2020 07:55:41: #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 07:55:41: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:55:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:55:49: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:56:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494945/SRX494945.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:56:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494945/SRX494945.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:56:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494945/SRX494945.10_summits.bed INFO @ Fri, 26 Jun 2020 07:56:05: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:56:16: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:56:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494945/SRX494945.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:56:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494945/SRX494945.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:56:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494945/SRX494945.20_summits.bed INFO @ Fri, 26 Jun 2020 07:56:31: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling