Job ID = 6507889 SRX = SRX494974 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:18:03 prefetch.2.10.7: 1) Downloading 'SRR1198506'... 2020-06-26T13:18:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:32:47 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:32:47 prefetch.2.10.7: 1) 'SRR1198506' was downloaded successfully 2020-06-26T13:32:47 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: 00:16:46 40075123 reads; of these: 40075123 (100.00%) were unpaired; of these: 1275952 (3.18%) aligned 0 times 32482016 (81.05%) aligned exactly 1 time 6317155 (15.76%) aligned >1 times 96.82% overall alignment rate Time searching: 00:16:46 Overall time: 00:16:46 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] 20130999 / 38799171 = 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 23:06:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494974/SRX494974.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494974/SRX494974.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494974/SRX494974.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 23:06:11: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:06:11: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:06:19: 1000000 INFO @ Fri, 26 Jun 2020 23:06:26: 2000000 INFO @ Fri, 26 Jun 2020 23:06:34: 3000000 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 23:06:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494974/SRX494974.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494974/SRX494974.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494974/SRX494974.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 23:06:41: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:06:41: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:06:41: 4000000 INFO @ Fri, 26 Jun 2020 23:06:50: 1000000 INFO @ Fri, 26 Jun 2020 23:06:50: 5000000 INFO @ Fri, 26 Jun 2020 23:06:58: 2000000 INFO @ Fri, 26 Jun 2020 23:06:58: 6000000 INFO @ Fri, 26 Jun 2020 23:07:06: 3000000 INFO @ Fri, 26 Jun 2020 23:07:06: 7000000 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 23:07:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494974/SRX494974.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494974/SRX494974.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494974/SRX494974.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 23:07:11: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:07:11: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:07:15: 8000000 INFO @ Fri, 26 Jun 2020 23:07:15: 4000000 INFO @ Fri, 26 Jun 2020 23:07:20: 1000000 INFO @ Fri, 26 Jun 2020 23:07:23: 9000000 INFO @ Fri, 26 Jun 2020 23:07:23: 5000000 INFO @ Fri, 26 Jun 2020 23:07:28: 2000000 INFO @ Fri, 26 Jun 2020 23:07:32: 10000000 INFO @ Fri, 26 Jun 2020 23:07:32: 6000000 INFO @ Fri, 26 Jun 2020 23:07:37: 3000000 INFO @ Fri, 26 Jun 2020 23:07:40: 11000000 INFO @ Fri, 26 Jun 2020 23:07:41: 7000000 INFO @ Fri, 26 Jun 2020 23:07:45: 4000000 INFO @ Fri, 26 Jun 2020 23:07:49: 12000000 INFO @ Fri, 26 Jun 2020 23:07:50: 8000000 INFO @ Fri, 26 Jun 2020 23:07:54: 5000000 INFO @ Fri, 26 Jun 2020 23:07:57: 13000000 INFO @ Fri, 26 Jun 2020 23:07:59: 9000000 INFO @ Fri, 26 Jun 2020 23:08:02: 6000000 INFO @ Fri, 26 Jun 2020 23:08:06: 14000000 INFO @ Fri, 26 Jun 2020 23:08:07: 10000000 INFO @ Fri, 26 Jun 2020 23:08:10: 7000000 INFO @ Fri, 26 Jun 2020 23:08:14: 15000000 INFO @ Fri, 26 Jun 2020 23:08:16: 11000000 INFO @ Fri, 26 Jun 2020 23:08:19: 8000000 INFO @ Fri, 26 Jun 2020 23:08:22: 16000000 INFO @ Fri, 26 Jun 2020 23:08:25: 12000000 INFO @ Fri, 26 Jun 2020 23:08:27: 9000000 INFO @ Fri, 26 Jun 2020 23:08:31: 17000000 INFO @ Fri, 26 Jun 2020 23:08:34: 13000000 INFO @ Fri, 26 Jun 2020 23:08:36: 10000000 INFO @ Fri, 26 Jun 2020 23:08:39: 18000000 INFO @ Fri, 26 Jun 2020 23:08:43: 14000000 INFO @ Fri, 26 Jun 2020 23:08:44: 11000000 INFO @ Fri, 26 Jun 2020 23:08:44: #1 tag size is determined as 75 bps INFO @ Fri, 26 Jun 2020 23:08:44: #1 tag size = 75 INFO @ Fri, 26 Jun 2020 23:08:44: #1 total tags in treatment: 18668172 INFO @ Fri, 26 Jun 2020 23:08:44: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:08:44: #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 23:08:45: #1 tags after filtering in treatment: 18668172 INFO @ Fri, 26 Jun 2020 23:08:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:08:45: #1 finished! INFO @ Fri, 26 Jun 2020 23:08:45: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:08:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:08:46: #2 number of paired peaks: 290 WARNING @ Fri, 26 Jun 2020 23:08:46: 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 23:08:46: start model_add_line... INFO @ Fri, 26 Jun 2020 23:08:46: start X-correlation... INFO @ Fri, 26 Jun 2020 23:08:46: end of X-cor INFO @ Fri, 26 Jun 2020 23:08:46: #2 finished! INFO @ Fri, 26 Jun 2020 23:08:46: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:08:46: #2 alternative fragment length(s) may be 1,31,583 bps INFO @ Fri, 26 Jun 2020 23:08:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494974/SRX494974.05_model.r WARNING @ Fri, 26 Jun 2020 23:08:46: #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 23:08:46: #2 You may need to consider one of the other alternative d(s): 1,31,583 WARNING @ Fri, 26 Jun 2020 23:08:46: #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 23:08:46: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:08:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:08:51: 15000000 INFO @ Fri, 26 Jun 2020 23:08:52: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:09:00: 16000000 INFO @ Fri, 26 Jun 2020 23:09:01: 13000000 INFO @ Fri, 26 Jun 2020 23:09:08: 17000000 INFO @ Fri, 26 Jun 2020 23:09:09: 14000000 INFO @ Fri, 26 Jun 2020 23:09:17: 18000000 INFO @ Fri, 26 Jun 2020 23:09:17: 15000000 INFO @ Fri, 26 Jun 2020 23:09:21: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:09:23: #1 tag size is determined as 75 bps INFO @ Fri, 26 Jun 2020 23:09:23: #1 tag size = 75 INFO @ Fri, 26 Jun 2020 23:09:23: #1 total tags in treatment: 18668172 INFO @ Fri, 26 Jun 2020 23:09:23: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:09:23: #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 23:09:23: #1 tags after filtering in treatment: 18668172 INFO @ Fri, 26 Jun 2020 23:09:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:09:23: #1 finished! INFO @ Fri, 26 Jun 2020 23:09:23: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:09:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:09:24: #2 number of paired peaks: 290 WARNING @ Fri, 26 Jun 2020 23:09:24: 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 23:09:24: start model_add_line... INFO @ Fri, 26 Jun 2020 23:09:25: start X-correlation... INFO @ Fri, 26 Jun 2020 23:09:25: end of X-cor INFO @ Fri, 26 Jun 2020 23:09:25: #2 finished! INFO @ Fri, 26 Jun 2020 23:09:25: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:09:25: #2 alternative fragment length(s) may be 1,31,583 bps INFO @ Fri, 26 Jun 2020 23:09:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494974/SRX494974.10_model.r WARNING @ Fri, 26 Jun 2020 23:09:25: #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 23:09:25: #2 You may need to consider one of the other alternative d(s): 1,31,583 WARNING @ Fri, 26 Jun 2020 23:09:25: #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 23:09:25: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:09:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:09:26: 16000000 INFO @ Fri, 26 Jun 2020 23:09:33: 17000000 INFO @ Fri, 26 Jun 2020 23:09:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494974/SRX494974.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:09:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494974/SRX494974.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:09:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494974/SRX494974.05_summits.bed INFO @ Fri, 26 Jun 2020 23:09:37: 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 23:09:42: 18000000 INFO @ Fri, 26 Jun 2020 23:09:47: #1 tag size is determined as 75 bps INFO @ Fri, 26 Jun 2020 23:09:47: #1 tag size = 75 INFO @ Fri, 26 Jun 2020 23:09:47: #1 total tags in treatment: 18668172 INFO @ Fri, 26 Jun 2020 23:09:47: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:09:47: #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 23:09:47: #1 tags after filtering in treatment: 18668172 INFO @ Fri, 26 Jun 2020 23:09:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:09:47: #1 finished! INFO @ Fri, 26 Jun 2020 23:09:47: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:09:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:09:49: #2 number of paired peaks: 290 WARNING @ Fri, 26 Jun 2020 23:09:49: 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 23:09:49: start model_add_line... INFO @ Fri, 26 Jun 2020 23:09:49: start X-correlation... INFO @ Fri, 26 Jun 2020 23:09:49: end of X-cor INFO @ Fri, 26 Jun 2020 23:09:49: #2 finished! INFO @ Fri, 26 Jun 2020 23:09:49: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:09:49: #2 alternative fragment length(s) may be 1,31,583 bps INFO @ Fri, 26 Jun 2020 23:09:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494974/SRX494974.20_model.r WARNING @ Fri, 26 Jun 2020 23:09:49: #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 23:09:49: #2 You may need to consider one of the other alternative d(s): 1,31,583 WARNING @ Fri, 26 Jun 2020 23:09:49: #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 23:09:49: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:09:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:10:00: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:10:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494974/SRX494974.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:10:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494974/SRX494974.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:10:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494974/SRX494974.10_summits.bed INFO @ Fri, 26 Jun 2020 23:10:16: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:10:23: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:10:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494974/SRX494974.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:10:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494974/SRX494974.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:10:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494974/SRX494974.20_summits.bed INFO @ Fri, 26 Jun 2020 23:10:39: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling