Job ID = 6507878 SRX = SRX494963 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:11:12 prefetch.2.10.7: 1) Downloading 'SRR1198495'... 2020-06-26T14:11:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:13:39 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:13:39 prefetch.2.10.7: 1) 'SRR1198495' was downloaded successfully Read 22504141 spots for SRR1198495/SRR1198495.sra Written 22504141 spots for SRR1198495/SRR1198495.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: 00:05:12 22504141 reads; of these: 22504141 (100.00%) were unpaired; of these: 344765 (1.53%) aligned 0 times 18251421 (81.10%) aligned exactly 1 time 3907955 (17.37%) aligned >1 times 98.47% overall alignment rate Time searching: 00:05:12 Overall time: 00:05:12 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] 4553933 / 22159376 = 0.2055 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 23:24:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494963/SRX494963.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494963/SRX494963.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494963/SRX494963.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494963/SRX494963.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 23:24:50: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:24:50: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:24:56: 1000000 INFO @ Fri, 26 Jun 2020 23:25:01: 2000000 INFO @ Fri, 26 Jun 2020 23:25:07: 3000000 INFO @ Fri, 26 Jun 2020 23:25:12: 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 23:25:18: 5000000 INFO @ Fri, 26 Jun 2020 23:25:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494963/SRX494963.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494963/SRX494963.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494963/SRX494963.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494963/SRX494963.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 23:25:20: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:25:20: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:25:25: 6000000 INFO @ Fri, 26 Jun 2020 23:25:29: 1000000 INFO @ Fri, 26 Jun 2020 23:25:33: 7000000 INFO @ Fri, 26 Jun 2020 23:25:38: 2000000 INFO @ Fri, 26 Jun 2020 23:25:40: 8000000 INFO @ Fri, 26 Jun 2020 23:25:46: 3000000 INFO @ Fri, 26 Jun 2020 23:25:47: 9000000 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 23:25:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494963/SRX494963.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494963/SRX494963.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494963/SRX494963.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494963/SRX494963.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 23:25:50: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:25:50: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:25:55: 10000000 INFO @ Fri, 26 Jun 2020 23:25:55: 4000000 INFO @ Fri, 26 Jun 2020 23:25:59: 1000000 INFO @ Fri, 26 Jun 2020 23:26:02: 11000000 INFO @ Fri, 26 Jun 2020 23:26:04: 5000000 INFO @ Fri, 26 Jun 2020 23:26:08: 2000000 INFO @ Fri, 26 Jun 2020 23:26:10: 12000000 INFO @ Fri, 26 Jun 2020 23:26:12: 6000000 INFO @ Fri, 26 Jun 2020 23:26:16: 3000000 INFO @ Fri, 26 Jun 2020 23:26:18: 13000000 INFO @ Fri, 26 Jun 2020 23:26:21: 7000000 INFO @ Fri, 26 Jun 2020 23:26:25: 4000000 INFO @ Fri, 26 Jun 2020 23:26:25: 14000000 INFO @ Fri, 26 Jun 2020 23:26:30: 8000000 INFO @ Fri, 26 Jun 2020 23:26:33: 5000000 INFO @ Fri, 26 Jun 2020 23:26:33: 15000000 INFO @ Fri, 26 Jun 2020 23:26:38: 9000000 INFO @ Fri, 26 Jun 2020 23:26:41: 16000000 INFO @ Fri, 26 Jun 2020 23:26:42: 6000000 INFO @ Fri, 26 Jun 2020 23:26:47: 10000000 INFO @ Fri, 26 Jun 2020 23:26:49: 17000000 INFO @ Fri, 26 Jun 2020 23:26:50: 7000000 INFO @ Fri, 26 Jun 2020 23:26:54: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:26:54: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:26:54: #1 total tags in treatment: 17605443 INFO @ Fri, 26 Jun 2020 23:26:54: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:26:54: #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 23:26:54: #1 tags after filtering in treatment: 17605443 INFO @ Fri, 26 Jun 2020 23:26:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:26:54: #1 finished! INFO @ Fri, 26 Jun 2020 23:26:54: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:26:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:26:55: 11000000 INFO @ Fri, 26 Jun 2020 23:26:55: #2 number of paired peaks: 283 WARNING @ Fri, 26 Jun 2020 23:26:55: Fewer paired peaks (283) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 283 pairs to build model! INFO @ Fri, 26 Jun 2020 23:26:55: start model_add_line... INFO @ Fri, 26 Jun 2020 23:26:55: start X-correlation... INFO @ Fri, 26 Jun 2020 23:26:55: end of X-cor INFO @ Fri, 26 Jun 2020 23:26:55: #2 finished! INFO @ Fri, 26 Jun 2020 23:26:55: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:26:55: #2 alternative fragment length(s) may be 1,37 bps INFO @ Fri, 26 Jun 2020 23:26:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494963/SRX494963.05_model.r WARNING @ Fri, 26 Jun 2020 23:26:55: #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 23:26:55: #2 You may need to consider one of the other alternative d(s): 1,37 WARNING @ Fri, 26 Jun 2020 23:26:55: #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 23:26:55: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:26:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:26:58: 8000000 INFO @ Fri, 26 Jun 2020 23:27:03: 12000000 INFO @ Fri, 26 Jun 2020 23:27:07: 9000000 INFO @ Fri, 26 Jun 2020 23:27:10: 13000000 INFO @ Fri, 26 Jun 2020 23:27:15: 10000000 INFO @ Fri, 26 Jun 2020 23:27:18: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:27:22: 11000000 INFO @ Fri, 26 Jun 2020 23:27:26: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:27:26: 15000000 INFO @ Fri, 26 Jun 2020 23:27:30: 12000000 INFO @ Fri, 26 Jun 2020 23:27:34: 16000000 INFO @ Fri, 26 Jun 2020 23:27:38: 13000000 INFO @ Fri, 26 Jun 2020 23:27:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494963/SRX494963.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:27:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494963/SRX494963.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:27:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494963/SRX494963.05_summits.bed INFO @ Fri, 26 Jun 2020 23:27:40: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:27:41: 17000000 INFO @ Fri, 26 Jun 2020 23:27:45: 14000000 INFO @ Fri, 26 Jun 2020 23:27:45: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:27:45: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:27:45: #1 total tags in treatment: 17605443 INFO @ Fri, 26 Jun 2020 23:27:45: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:27:45: #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 23:27:45: #1 tags after filtering in treatment: 17605443 INFO @ Fri, 26 Jun 2020 23:27:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:27:45: #1 finished! INFO @ Fri, 26 Jun 2020 23:27:45: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:27:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:27:47: #2 number of paired peaks: 283 WARNING @ Fri, 26 Jun 2020 23:27:47: Fewer paired peaks (283) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 283 pairs to build model! INFO @ Fri, 26 Jun 2020 23:27:47: start model_add_line... INFO @ Fri, 26 Jun 2020 23:27:47: start X-correlation... INFO @ Fri, 26 Jun 2020 23:27:47: end of X-cor INFO @ Fri, 26 Jun 2020 23:27:47: #2 finished! INFO @ Fri, 26 Jun 2020 23:27:47: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:27:47: #2 alternative fragment length(s) may be 1,37 bps INFO @ Fri, 26 Jun 2020 23:27:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494963/SRX494963.10_model.r WARNING @ Fri, 26 Jun 2020 23:27:47: #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 23:27:47: #2 You may need to consider one of the other alternative d(s): 1,37 WARNING @ Fri, 26 Jun 2020 23:27:47: #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 23:27:47: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:27:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:27:52: 15000000 INFO @ Fri, 26 Jun 2020 23:27:58: 16000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:28:05: 17000000 INFO @ Fri, 26 Jun 2020 23:28:09: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:28:09: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:28:09: #1 total tags in treatment: 17605443 INFO @ Fri, 26 Jun 2020 23:28:09: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:28:09: #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 23:28:09: #1 tags after filtering in treatment: 17605443 INFO @ Fri, 26 Jun 2020 23:28:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:28:09: #1 finished! INFO @ Fri, 26 Jun 2020 23:28:09: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:28:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:28:11: #2 number of paired peaks: 283 WARNING @ Fri, 26 Jun 2020 23:28:11: Fewer paired peaks (283) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 283 pairs to build model! INFO @ Fri, 26 Jun 2020 23:28:11: start model_add_line... INFO @ Fri, 26 Jun 2020 23:28:11: start X-correlation... INFO @ Fri, 26 Jun 2020 23:28:11: end of X-cor INFO @ Fri, 26 Jun 2020 23:28:11: #2 finished! INFO @ Fri, 26 Jun 2020 23:28:11: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:28:11: #2 alternative fragment length(s) may be 1,37 bps INFO @ Fri, 26 Jun 2020 23:28:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494963/SRX494963.20_model.r WARNING @ Fri, 26 Jun 2020 23:28:11: #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 23:28:11: #2 You may need to consider one of the other alternative d(s): 1,37 WARNING @ Fri, 26 Jun 2020 23:28:11: #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 23:28:11: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:28:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:28:18: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:28:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494963/SRX494963.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:28:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494963/SRX494963.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:28:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494963/SRX494963.10_summits.bed INFO @ Fri, 26 Jun 2020 23:28:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:28:43: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:28:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494963/SRX494963.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:28:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494963/SRX494963.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:28:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494963/SRX494963.20_summits.bed INFO @ Fri, 26 Jun 2020 23:28:58: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling