Job ID = 6497359 SRX = SRX257670 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T21:53:29 prefetch.2.10.7: 1) Downloading 'SRR800681'... 2020-06-25T21:53:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:55:04 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:55:05 prefetch.2.10.7: 'SRR800681' is valid 2020-06-25T21:55:05 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:02:41 11537873 reads; of these: 11537873 (100.00%) were unpaired; of these: 793771 (6.88%) aligned 0 times 8865334 (76.84%) aligned exactly 1 time 1878768 (16.28%) aligned >1 times 93.12% overall alignment rate Time searching: 00:02:44 Overall time: 00:02:45 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] 897785 / 10744102 = 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 07:01:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257670/SRX257670.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257670/SRX257670.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257670/SRX257670.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 07:01:46: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:01:46: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:01:53: 1000000 INFO @ Fri, 26 Jun 2020 07:02:00: 2000000 INFO @ Fri, 26 Jun 2020 07:02:07: 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 07:02:14: 4000000 INFO @ Fri, 26 Jun 2020 07:02:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257670/SRX257670.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257670/SRX257670.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257670/SRX257670.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 07:02:16: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:02:16: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:02:22: 5000000 INFO @ Fri, 26 Jun 2020 07:02:23: 1000000 INFO @ Fri, 26 Jun 2020 07:02:29: 6000000 INFO @ Fri, 26 Jun 2020 07:02:29: 2000000 INFO @ Fri, 26 Jun 2020 07:02:36: 3000000 INFO @ Fri, 26 Jun 2020 07:02:37: 7000000 INFO @ Fri, 26 Jun 2020 07:02:43: 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 @ Fri, 26 Jun 2020 07:02:44: 8000000 INFO @ Fri, 26 Jun 2020 07:02:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257670/SRX257670.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257670/SRX257670.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257670/SRX257670.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 07:02:46: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:02:46: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:02:50: 5000000 INFO @ Fri, 26 Jun 2020 07:02:51: 9000000 INFO @ Fri, 26 Jun 2020 07:02:53: 1000000 INFO @ Fri, 26 Jun 2020 07:02:57: 6000000 INFO @ Fri, 26 Jun 2020 07:02:57: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:02:57: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:02:57: #1 total tags in treatment: 9846317 INFO @ Fri, 26 Jun 2020 07:02:57: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:02:57: #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 07:02:58: #1 tags after filtering in treatment: 9846317 INFO @ Fri, 26 Jun 2020 07:02:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:02:58: #1 finished! INFO @ Fri, 26 Jun 2020 07:02:58: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:02:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:02:58: #2 number of paired peaks: 331 WARNING @ Fri, 26 Jun 2020 07:02:58: 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 07:02:58: start model_add_line... INFO @ Fri, 26 Jun 2020 07:02:58: start X-correlation... INFO @ Fri, 26 Jun 2020 07:02:58: end of X-cor INFO @ Fri, 26 Jun 2020 07:02:58: #2 finished! INFO @ Fri, 26 Jun 2020 07:02:58: #2 predicted fragment length is 50 bps INFO @ Fri, 26 Jun 2020 07:02:58: #2 alternative fragment length(s) may be 3,50 bps INFO @ Fri, 26 Jun 2020 07:02:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257670/SRX257670.05_model.r INFO @ Fri, 26 Jun 2020 07:03:00: 2000000 INFO @ Fri, 26 Jun 2020 07:03:03: 7000000 INFO @ Fri, 26 Jun 2020 07:03:07: 3000000 INFO @ Fri, 26 Jun 2020 07:03:10: 8000000 WARNING @ Fri, 26 Jun 2020 07:03:11: #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 07:03:11: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Fri, 26 Jun 2020 07:03:11: #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 07:03:11: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:03:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:03:13: 4000000 INFO @ Fri, 26 Jun 2020 07:03:16: 9000000 INFO @ Fri, 26 Jun 2020 07:03:20: 5000000 INFO @ Fri, 26 Jun 2020 07:03:22: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:03:22: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:03:22: #1 total tags in treatment: 9846317 INFO @ Fri, 26 Jun 2020 07:03:22: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:03:22: #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 07:03:22: #1 tags after filtering in treatment: 9846317 INFO @ Fri, 26 Jun 2020 07:03:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:03:22: #1 finished! INFO @ Fri, 26 Jun 2020 07:03:22: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:03:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:03:23: #2 number of paired peaks: 331 WARNING @ Fri, 26 Jun 2020 07:03:23: 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 07:03:23: start model_add_line... INFO @ Fri, 26 Jun 2020 07:03:23: start X-correlation... INFO @ Fri, 26 Jun 2020 07:03:23: end of X-cor INFO @ Fri, 26 Jun 2020 07:03:23: #2 finished! INFO @ Fri, 26 Jun 2020 07:03:23: #2 predicted fragment length is 50 bps INFO @ Fri, 26 Jun 2020 07:03:23: #2 alternative fragment length(s) may be 3,50 bps INFO @ Fri, 26 Jun 2020 07:03:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257670/SRX257670.10_model.r WARNING @ Fri, 26 Jun 2020 07:03:23: #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 07:03:23: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Fri, 26 Jun 2020 07:03:23: #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 07:03:23: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:03:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:03:26: 6000000 INFO @ Fri, 26 Jun 2020 07:03:32: 7000000 INFO @ Fri, 26 Jun 2020 07:03:33: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:03:38: 8000000 INFO @ Fri, 26 Jun 2020 07:03:45: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:03:45: 9000000 INFO @ Fri, 26 Jun 2020 07:03:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257670/SRX257670.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:03:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257670/SRX257670.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:03:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257670/SRX257670.05_summits.bed INFO @ Fri, 26 Jun 2020 07:03:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (628 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:03:50: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:03:50: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:03:50: #1 total tags in treatment: 9846317 INFO @ Fri, 26 Jun 2020 07:03:50: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:03:50: #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 07:03:50: #1 tags after filtering in treatment: 9846317 INFO @ Fri, 26 Jun 2020 07:03:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:03:50: #1 finished! INFO @ Fri, 26 Jun 2020 07:03:50: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:03:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:03:51: #2 number of paired peaks: 331 WARNING @ Fri, 26 Jun 2020 07:03:51: 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 07:03:51: start model_add_line... INFO @ Fri, 26 Jun 2020 07:03:51: start X-correlation... INFO @ Fri, 26 Jun 2020 07:03:51: end of X-cor INFO @ Fri, 26 Jun 2020 07:03:51: #2 finished! INFO @ Fri, 26 Jun 2020 07:03:51: #2 predicted fragment length is 50 bps INFO @ Fri, 26 Jun 2020 07:03:51: #2 alternative fragment length(s) may be 3,50 bps INFO @ Fri, 26 Jun 2020 07:03:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257670/SRX257670.20_model.r WARNING @ Fri, 26 Jun 2020 07:03:51: #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 07:03:51: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Fri, 26 Jun 2020 07:03:51: #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 07:03:51: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:03:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:03:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257670/SRX257670.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:03:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257670/SRX257670.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:03:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257670/SRX257670.10_summits.bed INFO @ Fri, 26 Jun 2020 07:03:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (414 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:04:12: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:04:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257670/SRX257670.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:04:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257670/SRX257670.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:04:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257670/SRX257670.20_summits.bed INFO @ Fri, 26 Jun 2020 07:04:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (173 records, 4 fields): 2 millis CompletedMACS2peakCalling