Job ID = 6507749 SRX = SRX257670 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:03:11 prefetch.2.10.7: 1) Downloading 'SRR800681'... 2020-06-26T13:03:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:04:13 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:04:14 prefetch.2.10.7: 'SRR800681' is valid 2020-06-26T13:04:14 prefetch.2.10.7: 1) 'SRR800681' was downloaded successfully Read 11537873 spots for SRR800681/SRR800681.sra Written 11537873 spots for SRR800681/SRR800681.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:26 11537873 reads; of these: 11537873 (100.00%) were unpaired; of these: 793394 (6.88%) aligned 0 times 8865655 (76.84%) aligned exactly 1 time 1878824 (16.28%) aligned >1 times 93.12% overall alignment rate Time searching: 00:02:27 Overall time: 00:02:27 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] 897905 / 10744479 = 0.0836 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 22:10:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257670/SRX257670.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257670/SRX257670.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257670/SRX257670.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257670/SRX257670.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 22:10:22: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:10:22: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:10:30: 1000000 INFO @ Fri, 26 Jun 2020 22:10:38: 2000000 INFO @ Fri, 26 Jun 2020 22:10:45: 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 22:10:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257670/SRX257670.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257670/SRX257670.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257670/SRX257670.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257670/SRX257670.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 22:10:52: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:10:52: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:10:52: 4000000 INFO @ Fri, 26 Jun 2020 22:11:00: 1000000 INFO @ Fri, 26 Jun 2020 22:11:00: 5000000 INFO @ Fri, 26 Jun 2020 22:11:08: 2000000 INFO @ Fri, 26 Jun 2020 22:11:08: 6000000 INFO @ Fri, 26 Jun 2020 22:11:16: 3000000 INFO @ Fri, 26 Jun 2020 22:11:16: 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 22:11:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257670/SRX257670.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257670/SRX257670.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257670/SRX257670.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257670/SRX257670.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 22:11:22: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:11:22: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:11:24: 4000000 INFO @ Fri, 26 Jun 2020 22:11:24: 8000000 INFO @ Fri, 26 Jun 2020 22:11:30: 1000000 INFO @ Fri, 26 Jun 2020 22:11:32: 5000000 INFO @ Fri, 26 Jun 2020 22:11:32: 9000000 INFO @ Fri, 26 Jun 2020 22:11:37: 2000000 INFO @ Fri, 26 Jun 2020 22:11:39: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 22:11:39: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 22:11:39: #1 total tags in treatment: 9846574 INFO @ Fri, 26 Jun 2020 22:11:39: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:11:39: #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 22:11:39: #1 tags after filtering in treatment: 9846574 INFO @ Fri, 26 Jun 2020 22:11:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:11:39: #1 finished! INFO @ Fri, 26 Jun 2020 22:11:39: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:11:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:11:40: 6000000 INFO @ Fri, 26 Jun 2020 22:11:40: #2 number of paired peaks: 331 WARNING @ Fri, 26 Jun 2020 22:11:40: Fewer paired peaks (331) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 331 pairs to build model! INFO @ Fri, 26 Jun 2020 22:11:40: start model_add_line... INFO @ Fri, 26 Jun 2020 22:11:40: start X-correlation... INFO @ Fri, 26 Jun 2020 22:11:40: end of X-cor INFO @ Fri, 26 Jun 2020 22:11:40: #2 finished! INFO @ Fri, 26 Jun 2020 22:11:40: #2 predicted fragment length is 50 bps INFO @ Fri, 26 Jun 2020 22:11:40: #2 alternative fragment length(s) may be 3,50 bps INFO @ Fri, 26 Jun 2020 22:11:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257670/SRX257670.05_model.r WARNING @ Fri, 26 Jun 2020 22:11:40: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:11:40: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Fri, 26 Jun 2020 22:11:40: #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 22:11:40: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:11:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:11:44: 3000000 INFO @ Fri, 26 Jun 2020 22:11:47: 7000000 INFO @ Fri, 26 Jun 2020 22:11:51: 4000000 INFO @ Fri, 26 Jun 2020 22:11:55: 8000000 INFO @ Fri, 26 Jun 2020 22:11:58: 5000000 INFO @ Fri, 26 Jun 2020 22:12:01: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:12:01: 9000000 INFO @ Fri, 26 Jun 2020 22:12:05: 6000000 INFO @ Fri, 26 Jun 2020 22:12:07: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 22:12:07: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 22:12:07: #1 total tags in treatment: 9846574 INFO @ Fri, 26 Jun 2020 22:12:07: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:12:07: #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 22:12:07: #1 tags after filtering in treatment: 9846574 INFO @ Fri, 26 Jun 2020 22:12:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:12:07: #1 finished! INFO @ Fri, 26 Jun 2020 22:12:07: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:12:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:12:08: #2 number of paired peaks: 331 WARNING @ Fri, 26 Jun 2020 22:12:08: Fewer paired peaks (331) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 331 pairs to build model! INFO @ Fri, 26 Jun 2020 22:12:08: start model_add_line... INFO @ Fri, 26 Jun 2020 22:12:08: start X-correlation... INFO @ Fri, 26 Jun 2020 22:12:08: end of X-cor INFO @ Fri, 26 Jun 2020 22:12:08: #2 finished! INFO @ Fri, 26 Jun 2020 22:12:08: #2 predicted fragment length is 50 bps INFO @ Fri, 26 Jun 2020 22:12:08: #2 alternative fragment length(s) may be 3,50 bps INFO @ Fri, 26 Jun 2020 22:12:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257670/SRX257670.10_model.r WARNING @ Fri, 26 Jun 2020 22:12:08: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:12:08: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Fri, 26 Jun 2020 22:12:08: #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 22:12:08: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:12:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:12:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257670/SRX257670.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:12:11: 7000000 INFO @ Fri, 26 Jun 2020 22:12:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257670/SRX257670.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:12:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257670/SRX257670.05_summits.bed INFO @ Fri, 26 Jun 2020 22:12:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (627 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:12:17: 8000000 INFO @ Fri, 26 Jun 2020 22:12:23: 9000000 INFO @ Fri, 26 Jun 2020 22:12:27: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:12:28: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 22:12:28: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 22:12:28: #1 total tags in treatment: 9846574 INFO @ Fri, 26 Jun 2020 22:12:28: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:12:28: #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 22:12:28: #1 tags after filtering in treatment: 9846574 INFO @ Fri, 26 Jun 2020 22:12:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:12:28: #1 finished! INFO @ Fri, 26 Jun 2020 22:12:28: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:12:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:12:28: #2 number of paired peaks: 331 WARNING @ Fri, 26 Jun 2020 22:12:28: Fewer paired peaks (331) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 331 pairs to build model! INFO @ Fri, 26 Jun 2020 22:12:28: start model_add_line... INFO @ Fri, 26 Jun 2020 22:12:28: start X-correlation... INFO @ Fri, 26 Jun 2020 22:12:28: end of X-cor INFO @ Fri, 26 Jun 2020 22:12:28: #2 finished! INFO @ Fri, 26 Jun 2020 22:12:28: #2 predicted fragment length is 50 bps INFO @ Fri, 26 Jun 2020 22:12:28: #2 alternative fragment length(s) may be 3,50 bps INFO @ Fri, 26 Jun 2020 22:12:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257670/SRX257670.20_model.r WARNING @ Fri, 26 Jun 2020 22:12:28: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:12:28: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Fri, 26 Jun 2020 22:12:28: #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 22:12:28: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:12:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:12:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257670/SRX257670.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:12:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257670/SRX257670.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:12:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257670/SRX257670.10_summits.bed INFO @ Fri, 26 Jun 2020 22:12:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (414 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:12:49: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:12:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257670/SRX257670.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:12:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257670/SRX257670.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:12:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257670/SRX257670.20_summits.bed INFO @ Fri, 26 Jun 2020 22:12:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (172 records, 4 fields): 1 millis CompletedMACS2peakCalling