Job ID = 6497449 SRX = SRX494947 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:37:20 prefetch.2.10.7: 1) Downloading 'SRR1198479'... 2020-06-25T22:37:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:39:10 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:39:11 prefetch.2.10.7: 'SRR1198479' is valid 2020-06-25T22:39:11 prefetch.2.10.7: 1) 'SRR1198479' was downloaded successfully Read 15863850 spots for SRR1198479/SRR1198479.sra Written 15863850 spots for SRR1198479/SRR1198479.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: 00:03:27 15863850 reads; of these: 15863850 (100.00%) were unpaired; of these: 232785 (1.47%) aligned 0 times 12989351 (81.88%) aligned exactly 1 time 2641714 (16.65%) aligned >1 times 98.53% overall alignment rate Time searching: 00:03:27 Overall time: 00:03:27 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] 1436269 / 15631065 = 0.0919 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 07:48:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494947/SRX494947.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494947/SRX494947.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494947/SRX494947.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494947/SRX494947.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 07:48:16: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:48:16: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:48:22: 1000000 INFO @ Fri, 26 Jun 2020 07:48:29: 2000000 INFO @ Fri, 26 Jun 2020 07:48:36: 3000000 INFO @ Fri, 26 Jun 2020 07:48:43: 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 07:48:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494947/SRX494947.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494947/SRX494947.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494947/SRX494947.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494947/SRX494947.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 07:48:45: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:48:45: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:48:50: 5000000 INFO @ Fri, 26 Jun 2020 07:48:53: 1000000 INFO @ Fri, 26 Jun 2020 07:48:57: 6000000 INFO @ Fri, 26 Jun 2020 07:49:00: 2000000 INFO @ Fri, 26 Jun 2020 07:49:05: 7000000 INFO @ Fri, 26 Jun 2020 07:49:07: 3000000 INFO @ Fri, 26 Jun 2020 07:49:12: 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 07:49:14: 4000000 INFO @ Fri, 26 Jun 2020 07:49:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494947/SRX494947.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494947/SRX494947.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494947/SRX494947.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494947/SRX494947.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 07:49:15: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:49:15: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:49:19: 9000000 INFO @ Fri, 26 Jun 2020 07:49:22: 5000000 INFO @ Fri, 26 Jun 2020 07:49:23: 1000000 INFO @ Fri, 26 Jun 2020 07:49:27: 10000000 INFO @ Fri, 26 Jun 2020 07:49:29: 6000000 INFO @ Fri, 26 Jun 2020 07:49:30: 2000000 INFO @ Fri, 26 Jun 2020 07:49:34: 11000000 INFO @ Fri, 26 Jun 2020 07:49:37: 7000000 INFO @ Fri, 26 Jun 2020 07:49:38: 3000000 INFO @ Fri, 26 Jun 2020 07:49:42: 12000000 INFO @ Fri, 26 Jun 2020 07:49:45: 8000000 INFO @ Fri, 26 Jun 2020 07:49:45: 4000000 INFO @ Fri, 26 Jun 2020 07:49:50: 13000000 INFO @ Fri, 26 Jun 2020 07:49:52: 9000000 INFO @ Fri, 26 Jun 2020 07:49:53: 5000000 INFO @ Fri, 26 Jun 2020 07:49:57: 14000000 INFO @ Fri, 26 Jun 2020 07:49:59: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:49:59: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:49:59: #1 total tags in treatment: 14194796 INFO @ Fri, 26 Jun 2020 07:49:59: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:49:59: #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 07:49:59: #1 tags after filtering in treatment: 14194796 INFO @ Fri, 26 Jun 2020 07:49:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:49:59: #1 finished! INFO @ Fri, 26 Jun 2020 07:49:59: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:49:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:50:00: 10000000 INFO @ Fri, 26 Jun 2020 07:50:00: 6000000 INFO @ Fri, 26 Jun 2020 07:50:00: #2 number of paired peaks: 252 WARNING @ Fri, 26 Jun 2020 07:50:00: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Fri, 26 Jun 2020 07:50:00: start model_add_line... INFO @ Fri, 26 Jun 2020 07:50:00: start X-correlation... INFO @ Fri, 26 Jun 2020 07:50:00: end of X-cor INFO @ Fri, 26 Jun 2020 07:50:00: #2 finished! INFO @ Fri, 26 Jun 2020 07:50:00: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:50:00: #2 alternative fragment length(s) may be 1,30,559,596 bps INFO @ Fri, 26 Jun 2020 07:50:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494947/SRX494947.05_model.r WARNING @ Fri, 26 Jun 2020 07:50:00: #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 07:50:00: #2 You may need to consider one of the other alternative d(s): 1,30,559,596 WARNING @ Fri, 26 Jun 2020 07:50:00: #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 07:50:00: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:50:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:50:07: 11000000 INFO @ Fri, 26 Jun 2020 07:50:07: 7000000 INFO @ Fri, 26 Jun 2020 07:50:15: 12000000 INFO @ Fri, 26 Jun 2020 07:50:15: 8000000 INFO @ Fri, 26 Jun 2020 07:50:22: 13000000 INFO @ Fri, 26 Jun 2020 07:50:22: 9000000 INFO @ Fri, 26 Jun 2020 07:50:29: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:50:29: 14000000 INFO @ Fri, 26 Jun 2020 07:50:29: 10000000 INFO @ Fri, 26 Jun 2020 07:50:31: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:50:31: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:50:31: #1 total tags in treatment: 14194796 INFO @ Fri, 26 Jun 2020 07:50:31: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:50:31: #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 07:50:31: #1 tags after filtering in treatment: 14194796 INFO @ Fri, 26 Jun 2020 07:50:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:50:31: #1 finished! INFO @ Fri, 26 Jun 2020 07:50:31: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:50:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:50:32: #2 number of paired peaks: 252 WARNING @ Fri, 26 Jun 2020 07:50:32: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Fri, 26 Jun 2020 07:50:32: start model_add_line... INFO @ Fri, 26 Jun 2020 07:50:32: start X-correlation... INFO @ Fri, 26 Jun 2020 07:50:32: end of X-cor INFO @ Fri, 26 Jun 2020 07:50:32: #2 finished! INFO @ Fri, 26 Jun 2020 07:50:32: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:50:32: #2 alternative fragment length(s) may be 1,30,559,596 bps INFO @ Fri, 26 Jun 2020 07:50:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494947/SRX494947.10_model.r WARNING @ Fri, 26 Jun 2020 07:50:32: #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 07:50:32: #2 You may need to consider one of the other alternative d(s): 1,30,559,596 WARNING @ Fri, 26 Jun 2020 07:50:32: #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 07:50:32: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:50:32: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:50:36: 11000000 INFO @ Fri, 26 Jun 2020 07:50:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494947/SRX494947.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:50:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494947/SRX494947.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:50:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494947/SRX494947.05_summits.bed INFO @ Fri, 26 Jun 2020 07:50:42: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:50:43: 12000000 INFO @ Fri, 26 Jun 2020 07:50:50: 13000000 INFO @ Fri, 26 Jun 2020 07:50:57: 14000000 INFO @ Fri, 26 Jun 2020 07:50:58: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:50:58: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:50:58: #1 total tags in treatment: 14194796 INFO @ Fri, 26 Jun 2020 07:50:58: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:50:58: #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 07:50:59: #1 tags after filtering in treatment: 14194796 INFO @ Fri, 26 Jun 2020 07:50:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:50:59: #1 finished! INFO @ Fri, 26 Jun 2020 07:50:59: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:50:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:51:00: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:51:00: #2 number of paired peaks: 252 WARNING @ Fri, 26 Jun 2020 07:51:00: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Fri, 26 Jun 2020 07:51:00: start model_add_line... INFO @ Fri, 26 Jun 2020 07:51:00: start X-correlation... INFO @ Fri, 26 Jun 2020 07:51:00: end of X-cor INFO @ Fri, 26 Jun 2020 07:51:00: #2 finished! INFO @ Fri, 26 Jun 2020 07:51:00: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:51:00: #2 alternative fragment length(s) may be 1,30,559,596 bps INFO @ Fri, 26 Jun 2020 07:51:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494947/SRX494947.20_model.r WARNING @ Fri, 26 Jun 2020 07:51:00: #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 07:51:00: #2 You may need to consider one of the other alternative d(s): 1,30,559,596 WARNING @ Fri, 26 Jun 2020 07:51:00: #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 07:51:00: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:51:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:51:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494947/SRX494947.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:51:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494947/SRX494947.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:51:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494947/SRX494947.10_summits.bed INFO @ Fri, 26 Jun 2020 07:51:13: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:51:28: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:51:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494947/SRX494947.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:51:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494947/SRX494947.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:51:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494947/SRX494947.20_summits.bed INFO @ Fri, 26 Jun 2020 07:51:41: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling