Job ID = 6368172 SRX = SRX494856 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:04:30 prefetch.2.10.7: 1) Downloading 'SRR1198388'... 2020-06-16T00:04:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:07:18 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:07:18 prefetch.2.10.7: 1) 'SRR1198388' was downloaded successfully Read 20117538 spots for SRR1198388/SRR1198388.sra Written 20117538 spots for SRR1198388/SRR1198388.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: 00:04:39 20117538 reads; of these: 20117538 (100.00%) were unpaired; of these: 1021637 (5.08%) aligned 0 times 15666575 (77.88%) aligned exactly 1 time 3429326 (17.05%) aligned >1 times 94.92% overall alignment rate Time searching: 00:04:39 Overall time: 00:04:39 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] 2624735 / 19095901 = 0.1375 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 09:19:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494856/SRX494856.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494856/SRX494856.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494856/SRX494856.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494856/SRX494856.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 09:19:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:26: 1000000 INFO @ Tue, 16 Jun 2020 09:19:30: 2000000 INFO @ Tue, 16 Jun 2020 09:19:35: 3000000 INFO @ Tue, 16 Jun 2020 09:19:40: 4000000 INFO @ Tue, 16 Jun 2020 09:19:45: 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 09:19:50: 6000000 INFO @ Tue, 16 Jun 2020 09:19:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494856/SRX494856.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494856/SRX494856.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494856/SRX494856.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494856/SRX494856.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 09:19:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:55: 7000000 INFO @ Tue, 16 Jun 2020 09:19:56: 1000000 INFO @ Tue, 16 Jun 2020 09:20:00: 8000000 INFO @ Tue, 16 Jun 2020 09:20:01: 2000000 INFO @ Tue, 16 Jun 2020 09:20:05: 9000000 INFO @ Tue, 16 Jun 2020 09:20:06: 3000000 INFO @ Tue, 16 Jun 2020 09:20:10: 10000000 INFO @ Tue, 16 Jun 2020 09:20:11: 4000000 INFO @ Tue, 16 Jun 2020 09:20:15: 11000000 INFO @ Tue, 16 Jun 2020 09:20:16: 5000000 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 09:20:20: 12000000 INFO @ Tue, 16 Jun 2020 09:20:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494856/SRX494856.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494856/SRX494856.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494856/SRX494856.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494856/SRX494856.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 09:20:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:20:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:20:22: 6000000 INFO @ Tue, 16 Jun 2020 09:20:26: 13000000 INFO @ Tue, 16 Jun 2020 09:20:27: 1000000 INFO @ Tue, 16 Jun 2020 09:20:27: 7000000 INFO @ Tue, 16 Jun 2020 09:20:32: 14000000 INFO @ Tue, 16 Jun 2020 09:20:32: 2000000 INFO @ Tue, 16 Jun 2020 09:20:33: 8000000 INFO @ Tue, 16 Jun 2020 09:20:38: 15000000 INFO @ Tue, 16 Jun 2020 09:20:38: 3000000 INFO @ Tue, 16 Jun 2020 09:20:39: 9000000 INFO @ Tue, 16 Jun 2020 09:20:44: 16000000 INFO @ Tue, 16 Jun 2020 09:20:44: 4000000 INFO @ Tue, 16 Jun 2020 09:20:44: 10000000 INFO @ Tue, 16 Jun 2020 09:20:47: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:20:47: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:20:47: #1 total tags in treatment: 16471166 INFO @ Tue, 16 Jun 2020 09:20:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:47: #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 09:20:47: #1 tags after filtering in treatment: 16471166 INFO @ Tue, 16 Jun 2020 09:20:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:47: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:48: #2 number of paired peaks: 231 WARNING @ Tue, 16 Jun 2020 09:20:48: Fewer paired peaks (231) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 231 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:48: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:48: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:48: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:48: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:48: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 09:20:48: #2 alternative fragment length(s) may be 1,46,511,593 bps INFO @ Tue, 16 Jun 2020 09:20:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494856/SRX494856.05_model.r WARNING @ Tue, 16 Jun 2020 09:20:48: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:20:48: #2 You may need to consider one of the other alternative d(s): 1,46,511,593 WARNING @ Tue, 16 Jun 2020 09:20:48: #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 09:20:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:20:49: 5000000 INFO @ Tue, 16 Jun 2020 09:20:50: 11000000 INFO @ Tue, 16 Jun 2020 09:20:55: 6000000 INFO @ Tue, 16 Jun 2020 09:20:55: 12000000 INFO @ Tue, 16 Jun 2020 09:21:00: 13000000 INFO @ Tue, 16 Jun 2020 09:21:00: 7000000 INFO @ Tue, 16 Jun 2020 09:21:05: 14000000 INFO @ Tue, 16 Jun 2020 09:21:05: 8000000 INFO @ Tue, 16 Jun 2020 09:21:10: 15000000 INFO @ Tue, 16 Jun 2020 09:21:10: 9000000 INFO @ Tue, 16 Jun 2020 09:21:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:21:15: 16000000 INFO @ Tue, 16 Jun 2020 09:21:15: 10000000 INFO @ Tue, 16 Jun 2020 09:21:18: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:21:18: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:21:18: #1 total tags in treatment: 16471166 INFO @ Tue, 16 Jun 2020 09:21:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:21:18: #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 09:21:18: #1 tags after filtering in treatment: 16471166 INFO @ Tue, 16 Jun 2020 09:21:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:21:18: #1 finished! INFO @ Tue, 16 Jun 2020 09:21:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:21:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:21:19: #2 number of paired peaks: 231 WARNING @ Tue, 16 Jun 2020 09:21:19: Fewer paired peaks (231) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 231 pairs to build model! INFO @ Tue, 16 Jun 2020 09:21:19: start model_add_line... INFO @ Tue, 16 Jun 2020 09:21:19: start X-correlation... INFO @ Tue, 16 Jun 2020 09:21:19: end of X-cor INFO @ Tue, 16 Jun 2020 09:21:19: #2 finished! INFO @ Tue, 16 Jun 2020 09:21:19: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 09:21:19: #2 alternative fragment length(s) may be 1,46,511,593 bps INFO @ Tue, 16 Jun 2020 09:21:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494856/SRX494856.10_model.r WARNING @ Tue, 16 Jun 2020 09:21:19: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:21:19: #2 You may need to consider one of the other alternative d(s): 1,46,511,593 WARNING @ Tue, 16 Jun 2020 09:21:19: #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 09:21:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:21:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:21:20: 11000000 INFO @ Tue, 16 Jun 2020 09:21:25: 12000000 INFO @ Tue, 16 Jun 2020 09:21:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494856/SRX494856.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494856/SRX494856.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494856/SRX494856.05_summits.bed INFO @ Tue, 16 Jun 2020 09:21:28: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (644 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:21:30: 13000000 INFO @ Tue, 16 Jun 2020 09:21:35: 14000000 INFO @ Tue, 16 Jun 2020 09:21:40: 15000000 INFO @ Tue, 16 Jun 2020 09:21:45: 16000000 INFO @ Tue, 16 Jun 2020 09:21:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:21:47: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:21:47: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:21:47: #1 total tags in treatment: 16471166 INFO @ Tue, 16 Jun 2020 09:21:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:21:47: #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 09:21:47: #1 tags after filtering in treatment: 16471166 INFO @ Tue, 16 Jun 2020 09:21:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:21:47: #1 finished! INFO @ Tue, 16 Jun 2020 09:21:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:21:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:21:48: #2 number of paired peaks: 231 WARNING @ Tue, 16 Jun 2020 09:21:48: Fewer paired peaks (231) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 231 pairs to build model! INFO @ Tue, 16 Jun 2020 09:21:48: start model_add_line... INFO @ Tue, 16 Jun 2020 09:21:49: start X-correlation... INFO @ Tue, 16 Jun 2020 09:21:49: end of X-cor INFO @ Tue, 16 Jun 2020 09:21:49: #2 finished! INFO @ Tue, 16 Jun 2020 09:21:49: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 09:21:49: #2 alternative fragment length(s) may be 1,46,511,593 bps INFO @ Tue, 16 Jun 2020 09:21:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494856/SRX494856.20_model.r WARNING @ Tue, 16 Jun 2020 09:21:49: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:21:49: #2 You may need to consider one of the other alternative d(s): 1,46,511,593 WARNING @ Tue, 16 Jun 2020 09:21:49: #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 09:21:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:21:49: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:21:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494856/SRX494856.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494856/SRX494856.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494856/SRX494856.10_summits.bed INFO @ Tue, 16 Jun 2020 09:21:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (415 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:22:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:22:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494856/SRX494856.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:22:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494856/SRX494856.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:22:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494856/SRX494856.20_summits.bed INFO @ Tue, 16 Jun 2020 09:22:27: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (142 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。