Job ID = 6497473 SRX = SRX494974 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:34:49 prefetch.2.10.7: 1) Downloading 'SRR1198506'... 2020-06-25T22:34:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:44:00 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:44:00 prefetch.2.10.7: 1) 'SRR1198506' was downloaded successfully 2020-06-25T22:44:00 prefetch.2.10.7: 'SRR1198506' has 0 unresolved dependencies Read 40075123 spots for SRR1198506/SRR1198506.sra Written 40075123 spots for SRR1198506/SRR1198506.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: 00:15:22 40075123 reads; of these: 40075123 (100.00%) were unpaired; of these: 1276356 (3.18%) aligned 0 times 32481730 (81.05%) aligned exactly 1 time 6317037 (15.76%) aligned >1 times 96.82% overall alignment rate Time searching: 00:15:22 Overall time: 00:15:22 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 16 files... [bam_rmdupse_core] 20130808 / 38798767 = 0.5189 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 08:15:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494974/SRX494974.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494974/SRX494974.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494974/SRX494974.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494974/SRX494974.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 08:15:17: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:15:17: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:15:23: 1000000 INFO @ Fri, 26 Jun 2020 08:15:29: 2000000 INFO @ Fri, 26 Jun 2020 08:15:35: 3000000 INFO @ Fri, 26 Jun 2020 08:15:41: 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 08:15:47: 5000000 INFO @ Fri, 26 Jun 2020 08:15:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494974/SRX494974.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494974/SRX494974.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494974/SRX494974.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494974/SRX494974.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 08:15:47: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:15:47: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:15:53: 6000000 INFO @ Fri, 26 Jun 2020 08:15:54: 1000000 INFO @ Fri, 26 Jun 2020 08:15:59: 7000000 INFO @ Fri, 26 Jun 2020 08:16:01: 2000000 INFO @ Fri, 26 Jun 2020 08:16:05: 8000000 INFO @ Fri, 26 Jun 2020 08:16:09: 3000000 INFO @ Fri, 26 Jun 2020 08:16:11: 9000000 BedGraph に変換中... INFO @ Fri, 26 Jun 2020 08:16:16: 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 08:16:17: 10000000 INFO @ Fri, 26 Jun 2020 08:16:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494974/SRX494974.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494974/SRX494974.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494974/SRX494974.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494974/SRX494974.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 08:16:18: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:16:18: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:16:23: 11000000 INFO @ Fri, 26 Jun 2020 08:16:23: 5000000 INFO @ Fri, 26 Jun 2020 08:16:26: 1000000 INFO @ Fri, 26 Jun 2020 08:16:29: 12000000 INFO @ Fri, 26 Jun 2020 08:16:31: 6000000 INFO @ Fri, 26 Jun 2020 08:16:33: 2000000 INFO @ Fri, 26 Jun 2020 08:16:35: 13000000 INFO @ Fri, 26 Jun 2020 08:16:38: 7000000 INFO @ Fri, 26 Jun 2020 08:16:40: 3000000 INFO @ Fri, 26 Jun 2020 08:16:41: 14000000 INFO @ Fri, 26 Jun 2020 08:16:46: 8000000 INFO @ Fri, 26 Jun 2020 08:16:47: 15000000 INFO @ Fri, 26 Jun 2020 08:16:48: 4000000 INFO @ Fri, 26 Jun 2020 08:16:53: 9000000 INFO @ Fri, 26 Jun 2020 08:16:53: 16000000 INFO @ Fri, 26 Jun 2020 08:16:55: 5000000 INFO @ Fri, 26 Jun 2020 08:16:59: 17000000 INFO @ Fri, 26 Jun 2020 08:17:00: 10000000 INFO @ Fri, 26 Jun 2020 08:17:02: 6000000 INFO @ Fri, 26 Jun 2020 08:17:05: 18000000 INFO @ Fri, 26 Jun 2020 08:17:08: 11000000 INFO @ Fri, 26 Jun 2020 08:17:09: 7000000 INFO @ Fri, 26 Jun 2020 08:17:10: #1 tag size is determined as 75 bps INFO @ Fri, 26 Jun 2020 08:17:10: #1 tag size = 75 INFO @ Fri, 26 Jun 2020 08:17:10: #1 total tags in treatment: 18667959 INFO @ Fri, 26 Jun 2020 08:17:10: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:17:10: #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 08:17:10: #1 tags after filtering in treatment: 18667959 INFO @ Fri, 26 Jun 2020 08:17:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:17:10: #1 finished! INFO @ Fri, 26 Jun 2020 08:17:10: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:17:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:17:11: #2 number of paired peaks: 290 WARNING @ Fri, 26 Jun 2020 08:17:11: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Fri, 26 Jun 2020 08:17:11: start model_add_line... INFO @ Fri, 26 Jun 2020 08:17:11: start X-correlation... INFO @ Fri, 26 Jun 2020 08:17:11: end of X-cor INFO @ Fri, 26 Jun 2020 08:17:11: #2 finished! INFO @ Fri, 26 Jun 2020 08:17:11: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 08:17:11: #2 alternative fragment length(s) may be 1,31,584 bps INFO @ Fri, 26 Jun 2020 08:17:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494974/SRX494974.05_model.r WARNING @ Fri, 26 Jun 2020 08:17:11: #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 08:17:11: #2 You may need to consider one of the other alternative d(s): 1,31,584 WARNING @ Fri, 26 Jun 2020 08:17:11: #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 08:17:11: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:17:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:17:15: 12000000 INFO @ Fri, 26 Jun 2020 08:17:17: 8000000 INFO @ Fri, 26 Jun 2020 08:17:23: 13000000 INFO @ Fri, 26 Jun 2020 08:17:24: 9000000 INFO @ Fri, 26 Jun 2020 08:17:30: 14000000 INFO @ Fri, 26 Jun 2020 08:17:31: 10000000 INFO @ Fri, 26 Jun 2020 08:17:37: 15000000 INFO @ Fri, 26 Jun 2020 08:17:38: 11000000 INFO @ Fri, 26 Jun 2020 08:17:45: 16000000 INFO @ Fri, 26 Jun 2020 08:17:45: 12000000 INFO @ Fri, 26 Jun 2020 08:17:45: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:17:52: 17000000 INFO @ Fri, 26 Jun 2020 08:17:52: 13000000 INFO @ Fri, 26 Jun 2020 08:17:59: 18000000 INFO @ Fri, 26 Jun 2020 08:18:00: 14000000 INFO @ Fri, 26 Jun 2020 08:18:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494974/SRX494974.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:18:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494974/SRX494974.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:18:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494974/SRX494974.05_summits.bed INFO @ Fri, 26 Jun 2020 08:18:01: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:18:05: #1 tag size is determined as 75 bps INFO @ Fri, 26 Jun 2020 08:18:05: #1 tag size = 75 INFO @ Fri, 26 Jun 2020 08:18:05: #1 total tags in treatment: 18667959 INFO @ Fri, 26 Jun 2020 08:18:05: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:18:05: #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 08:18:05: #1 tags after filtering in treatment: 18667959 INFO @ Fri, 26 Jun 2020 08:18:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:18:05: #1 finished! INFO @ Fri, 26 Jun 2020 08:18:05: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:18:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:18:06: #2 number of paired peaks: 290 WARNING @ Fri, 26 Jun 2020 08:18:06: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Fri, 26 Jun 2020 08:18:06: start model_add_line... INFO @ Fri, 26 Jun 2020 08:18:06: start X-correlation... INFO @ Fri, 26 Jun 2020 08:18:06: end of X-cor INFO @ Fri, 26 Jun 2020 08:18:06: #2 finished! INFO @ Fri, 26 Jun 2020 08:18:06: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 08:18:06: #2 alternative fragment length(s) may be 1,31,584 bps INFO @ Fri, 26 Jun 2020 08:18:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494974/SRX494974.10_model.r WARNING @ Fri, 26 Jun 2020 08:18:06: #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 08:18:06: #2 You may need to consider one of the other alternative d(s): 1,31,584 WARNING @ Fri, 26 Jun 2020 08:18:06: #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 08:18:06: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:18:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:18:07: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:18:14: 16000000 INFO @ Fri, 26 Jun 2020 08:18:21: 17000000 INFO @ Fri, 26 Jun 2020 08:18:28: 18000000 INFO @ Fri, 26 Jun 2020 08:18:33: #1 tag size is determined as 75 bps INFO @ Fri, 26 Jun 2020 08:18:33: #1 tag size = 75 INFO @ Fri, 26 Jun 2020 08:18:33: #1 total tags in treatment: 18667959 INFO @ Fri, 26 Jun 2020 08:18:33: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:18:33: #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 08:18:34: #1 tags after filtering in treatment: 18667959 INFO @ Fri, 26 Jun 2020 08:18:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:18:34: #1 finished! INFO @ Fri, 26 Jun 2020 08:18:34: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:18:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:18:35: #2 number of paired peaks: 290 WARNING @ Fri, 26 Jun 2020 08:18:35: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Fri, 26 Jun 2020 08:18:35: start model_add_line... INFO @ Fri, 26 Jun 2020 08:18:35: start X-correlation... INFO @ Fri, 26 Jun 2020 08:18:35: end of X-cor INFO @ Fri, 26 Jun 2020 08:18:35: #2 finished! INFO @ Fri, 26 Jun 2020 08:18:35: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 08:18:35: #2 alternative fragment length(s) may be 1,31,584 bps INFO @ Fri, 26 Jun 2020 08:18:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494974/SRX494974.20_model.r WARNING @ Fri, 26 Jun 2020 08:18:35: #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 08:18:35: #2 You may need to consider one of the other alternative d(s): 1,31,584 WARNING @ Fri, 26 Jun 2020 08:18:35: #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 08:18:35: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:18:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:18:41: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:18:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494974/SRX494974.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:18:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494974/SRX494974.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:18:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494974/SRX494974.10_summits.bed INFO @ Fri, 26 Jun 2020 08:18:57: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:19:10: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:19:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494974/SRX494974.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:19:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494974/SRX494974.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:19:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494974/SRX494974.20_summits.bed INFO @ Fri, 26 Jun 2020 08:19:27: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling