Job ID = 6366961 SRX = SRX2576660 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:00:53 prefetch.2.10.7: 1) Downloading 'SRR5272617'... 2020-06-15T23:00:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:02:06 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:02:07 prefetch.2.10.7: 'SRR5272617' is valid 2020-06-15T23:02:07 prefetch.2.10.7: 1) 'SRR5272617' was downloaded successfully Read 20026814 spots for SRR5272617/SRR5272617.sra Written 20026814 spots for SRR5272617/SRR5272617.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 20026814 reads; of these: 20026814 (100.00%) were unpaired; of these: 254467 (1.27%) aligned 0 times 16503724 (82.41%) aligned exactly 1 time 3268623 (16.32%) aligned >1 times 98.73% 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_sort_core] merging from 8 files... [bam_rmdupse_core] 2189934 / 19772347 = 0.1108 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 @ Tue, 16 Jun 2020 08:11:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576660/SRX2576660.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576660/SRX2576660.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576660/SRX2576660.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576660/SRX2576660.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 @ Tue, 16 Jun 2020 08:11:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:11:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:11:27: 1000000 INFO @ Tue, 16 Jun 2020 08:11:32: 2000000 INFO @ Tue, 16 Jun 2020 08:11:37: 3000000 INFO @ Tue, 16 Jun 2020 08:11:43: 4000000 INFO @ Tue, 16 Jun 2020 08:11:48: 5000000 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 @ Tue, 16 Jun 2020 08:11:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576660/SRX2576660.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576660/SRX2576660.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576660/SRX2576660.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576660/SRX2576660.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 @ Tue, 16 Jun 2020 08:11:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:11:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:11:54: 6000000 INFO @ Tue, 16 Jun 2020 08:11:58: 1000000 INFO @ Tue, 16 Jun 2020 08:12:01: 7000000 INFO @ Tue, 16 Jun 2020 08:12:05: 2000000 INFO @ Tue, 16 Jun 2020 08:12:07: 8000000 INFO @ Tue, 16 Jun 2020 08:12:12: 3000000 INFO @ Tue, 16 Jun 2020 08:12:14: 9000000 INFO @ Tue, 16 Jun 2020 08:12:19: 4000000 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 @ Tue, 16 Jun 2020 08:12:21: 10000000 INFO @ Tue, 16 Jun 2020 08:12:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576660/SRX2576660.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576660/SRX2576660.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576660/SRX2576660.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576660/SRX2576660.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 @ Tue, 16 Jun 2020 08:12:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:12:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:12:26: 5000000 INFO @ Tue, 16 Jun 2020 08:12:27: 11000000 INFO @ Tue, 16 Jun 2020 08:12:28: 1000000 INFO @ Tue, 16 Jun 2020 08:12:33: 6000000 INFO @ Tue, 16 Jun 2020 08:12:34: 12000000 INFO @ Tue, 16 Jun 2020 08:12:35: 2000000 INFO @ Tue, 16 Jun 2020 08:12:40: 7000000 INFO @ Tue, 16 Jun 2020 08:12:41: 13000000 INFO @ Tue, 16 Jun 2020 08:12:42: 3000000 INFO @ Tue, 16 Jun 2020 08:12:47: 8000000 INFO @ Tue, 16 Jun 2020 08:12:48: 14000000 INFO @ Tue, 16 Jun 2020 08:12:48: 4000000 INFO @ Tue, 16 Jun 2020 08:12:54: 15000000 INFO @ Tue, 16 Jun 2020 08:12:54: 9000000 INFO @ Tue, 16 Jun 2020 08:12:55: 5000000 INFO @ Tue, 16 Jun 2020 08:13:01: 16000000 INFO @ Tue, 16 Jun 2020 08:13:01: 10000000 INFO @ Tue, 16 Jun 2020 08:13:02: 6000000 INFO @ Tue, 16 Jun 2020 08:13:08: 17000000 INFO @ Tue, 16 Jun 2020 08:13:08: 11000000 INFO @ Tue, 16 Jun 2020 08:13:08: 7000000 INFO @ Tue, 16 Jun 2020 08:13:12: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:13:12: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:13:12: #1 total tags in treatment: 17582413 INFO @ Tue, 16 Jun 2020 08:13:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:13:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:13:12: #1 tags after filtering in treatment: 17582413 INFO @ Tue, 16 Jun 2020 08:13:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:13:12: #1 finished! INFO @ Tue, 16 Jun 2020 08:13:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:13:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:13:13: #2 number of paired peaks: 154 WARNING @ Tue, 16 Jun 2020 08:13:13: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Tue, 16 Jun 2020 08:13:13: start model_add_line... INFO @ Tue, 16 Jun 2020 08:13:13: start X-correlation... INFO @ Tue, 16 Jun 2020 08:13:13: end of X-cor INFO @ Tue, 16 Jun 2020 08:13:13: #2 finished! INFO @ Tue, 16 Jun 2020 08:13:13: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:13:13: #2 alternative fragment length(s) may be 1,31,540,569 bps INFO @ Tue, 16 Jun 2020 08:13:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576660/SRX2576660.05_model.r WARNING @ Tue, 16 Jun 2020 08:13:13: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:13:13: #2 You may need to consider one of the other alternative d(s): 1,31,540,569 WARNING @ Tue, 16 Jun 2020 08:13:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:13:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:13:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:13:15: 8000000 INFO @ Tue, 16 Jun 2020 08:13:15: 12000000 INFO @ Tue, 16 Jun 2020 08:13:22: 9000000 INFO @ Tue, 16 Jun 2020 08:13:22: 13000000 INFO @ Tue, 16 Jun 2020 08:13:29: 10000000 INFO @ Tue, 16 Jun 2020 08:13:29: 14000000 INFO @ Tue, 16 Jun 2020 08:13:36: 11000000 INFO @ Tue, 16 Jun 2020 08:13:36: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:13:42: 12000000 INFO @ Tue, 16 Jun 2020 08:13:43: 16000000 INFO @ Tue, 16 Jun 2020 08:13:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:13:49: 13000000 INFO @ Tue, 16 Jun 2020 08:13:50: 17000000 INFO @ Tue, 16 Jun 2020 08:13:54: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:13:54: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:13:54: #1 total tags in treatment: 17582413 INFO @ Tue, 16 Jun 2020 08:13:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:13:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:13:55: #1 tags after filtering in treatment: 17582413 INFO @ Tue, 16 Jun 2020 08:13:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:13:55: #1 finished! INFO @ Tue, 16 Jun 2020 08:13:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:13:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:13:56: 14000000 INFO @ Tue, 16 Jun 2020 08:13:56: #2 number of paired peaks: 154 WARNING @ Tue, 16 Jun 2020 08:13:56: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Tue, 16 Jun 2020 08:13:56: start model_add_line... INFO @ Tue, 16 Jun 2020 08:13:56: start X-correlation... INFO @ Tue, 16 Jun 2020 08:13:56: end of X-cor INFO @ Tue, 16 Jun 2020 08:13:56: #2 finished! INFO @ Tue, 16 Jun 2020 08:13:56: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:13:56: #2 alternative fragment length(s) may be 1,31,540,569 bps INFO @ Tue, 16 Jun 2020 08:13:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576660/SRX2576660.10_model.r WARNING @ Tue, 16 Jun 2020 08:13:56: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:13:56: #2 You may need to consider one of the other alternative d(s): 1,31,540,569 WARNING @ Tue, 16 Jun 2020 08:13:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:13:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:13:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:13:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576660/SRX2576660.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:13:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576660/SRX2576660.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:13:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576660/SRX2576660.05_summits.bed INFO @ Tue, 16 Jun 2020 08:13:58: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:14:01: 15000000 INFO @ Tue, 16 Jun 2020 08:14:07: 16000000 INFO @ Tue, 16 Jun 2020 08:14:13: 17000000 INFO @ Tue, 16 Jun 2020 08:14:17: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:14:17: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:14:17: #1 total tags in treatment: 17582413 INFO @ Tue, 16 Jun 2020 08:14:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:14:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:14:17: #1 tags after filtering in treatment: 17582413 INFO @ Tue, 16 Jun 2020 08:14:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:14:17: #1 finished! INFO @ Tue, 16 Jun 2020 08:14:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:14:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:14:18: #2 number of paired peaks: 154 WARNING @ Tue, 16 Jun 2020 08:14:18: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Tue, 16 Jun 2020 08:14:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:18: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:14:18: #2 alternative fragment length(s) may be 1,31,540,569 bps INFO @ Tue, 16 Jun 2020 08:14:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576660/SRX2576660.20_model.r WARNING @ Tue, 16 Jun 2020 08:14:18: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:14:18: #2 You may need to consider one of the other alternative d(s): 1,31,540,569 WARNING @ Tue, 16 Jun 2020 08:14:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:14:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:14:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:14:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576660/SRX2576660.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:14:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576660/SRX2576660.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:14:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576660/SRX2576660.10_summits.bed INFO @ Tue, 16 Jun 2020 08:14:38: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:14:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:15:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576660/SRX2576660.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576660/SRX2576660.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576660/SRX2576660.20_summits.bed INFO @ Tue, 16 Jun 2020 08:15:01: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling