Job ID = 6626434 SRX = SRX7262193 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:02:24 10852432 reads; of these: 10852432 (100.00%) were unpaired; of these: 749715 (6.91%) aligned 0 times 7940793 (73.17%) aligned exactly 1 time 2161924 (19.92%) aligned >1 times 93.09% overall alignment rate Time searching: 00:02:24 Overall time: 00:02:24 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] 1071594 / 10102717 = 0.1061 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, 14 Jul 2020 07:05:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262193/SRX7262193.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262193/SRX7262193.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262193/SRX7262193.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262193/SRX7262193.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, 14 Jul 2020 07:05:55: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:05:55: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:06:01: 1000000 INFO @ Tue, 14 Jul 2020 07:06:07: 2000000 INFO @ Tue, 14 Jul 2020 07:06:12: 3000000 INFO @ Tue, 14 Jul 2020 07:06:18: 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 @ Tue, 14 Jul 2020 07:06:24: 5000000 INFO @ Tue, 14 Jul 2020 07:06:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262193/SRX7262193.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262193/SRX7262193.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262193/SRX7262193.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262193/SRX7262193.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, 14 Jul 2020 07:06:25: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:06:25: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:06:30: 6000000 INFO @ Tue, 14 Jul 2020 07:06:32: 1000000 INFO @ Tue, 14 Jul 2020 07:06:36: 7000000 INFO @ Tue, 14 Jul 2020 07:06:38: 2000000 INFO @ Tue, 14 Jul 2020 07:06:42: 8000000 INFO @ Tue, 14 Jul 2020 07:06:45: 3000000 INFO @ Tue, 14 Jul 2020 07:06:49: 9000000 INFO @ Tue, 14 Jul 2020 07:06:49: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:06:49: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:06:49: #1 total tags in treatment: 9031123 INFO @ Tue, 14 Jul 2020 07:06:49: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:06:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:06:49: #1 tags after filtering in treatment: 9031123 INFO @ Tue, 14 Jul 2020 07:06:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:06:49: #1 finished! INFO @ Tue, 14 Jul 2020 07:06:49: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:06:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:06:50: #2 number of paired peaks: 402 WARNING @ Tue, 14 Jul 2020 07:06:50: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Tue, 14 Jul 2020 07:06:50: start model_add_line... INFO @ Tue, 14 Jul 2020 07:06:50: start X-correlation... INFO @ Tue, 14 Jul 2020 07:06:50: end of X-cor INFO @ Tue, 14 Jul 2020 07:06:50: #2 finished! INFO @ Tue, 14 Jul 2020 07:06:50: #2 predicted fragment length is 46 bps INFO @ Tue, 14 Jul 2020 07:06:50: #2 alternative fragment length(s) may be 2,46,542 bps INFO @ Tue, 14 Jul 2020 07:06:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262193/SRX7262193.05_model.r WARNING @ Tue, 14 Jul 2020 07:06:50: #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, 14 Jul 2020 07:06:50: #2 You may need to consider one of the other alternative d(s): 2,46,542 WARNING @ Tue, 14 Jul 2020 07:06:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:06:50: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:06:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:06:51: 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, 14 Jul 2020 07:06:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262193/SRX7262193.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262193/SRX7262193.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262193/SRX7262193.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262193/SRX7262193.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, 14 Jul 2020 07:06:55: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:06:55: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:06:57: 5000000 INFO @ Tue, 14 Jul 2020 07:07:02: 1000000 INFO @ Tue, 14 Jul 2020 07:07:03: 6000000 INFO @ Tue, 14 Jul 2020 07:07:08: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:07:08: 2000000 INFO @ Tue, 14 Jul 2020 07:07:09: 7000000 INFO @ Tue, 14 Jul 2020 07:07:15: 3000000 INFO @ Tue, 14 Jul 2020 07:07:16: 8000000 INFO @ Tue, 14 Jul 2020 07:07:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262193/SRX7262193.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:07:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262193/SRX7262193.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:07:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262193/SRX7262193.05_summits.bed INFO @ Tue, 14 Jul 2020 07:07:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (694 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:07:21: 4000000 INFO @ Tue, 14 Jul 2020 07:07:22: 9000000 INFO @ Tue, 14 Jul 2020 07:07:22: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:07:22: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:07:22: #1 total tags in treatment: 9031123 INFO @ Tue, 14 Jul 2020 07:07:22: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:07:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:07:22: #1 tags after filtering in treatment: 9031123 INFO @ Tue, 14 Jul 2020 07:07:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:07:22: #1 finished! INFO @ Tue, 14 Jul 2020 07:07:22: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:07:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:07:23: #2 number of paired peaks: 402 WARNING @ Tue, 14 Jul 2020 07:07:23: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Tue, 14 Jul 2020 07:07:23: start model_add_line... INFO @ Tue, 14 Jul 2020 07:07:23: start X-correlation... INFO @ Tue, 14 Jul 2020 07:07:23: end of X-cor INFO @ Tue, 14 Jul 2020 07:07:23: #2 finished! INFO @ Tue, 14 Jul 2020 07:07:23: #2 predicted fragment length is 46 bps INFO @ Tue, 14 Jul 2020 07:07:23: #2 alternative fragment length(s) may be 2,46,542 bps INFO @ Tue, 14 Jul 2020 07:07:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262193/SRX7262193.10_model.r WARNING @ Tue, 14 Jul 2020 07:07:23: #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, 14 Jul 2020 07:07:23: #2 You may need to consider one of the other alternative d(s): 2,46,542 WARNING @ Tue, 14 Jul 2020 07:07:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:07:23: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:07:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:07:27: 5000000 INFO @ Tue, 14 Jul 2020 07:07:33: 6000000 INFO @ Tue, 14 Jul 2020 07:07:39: 7000000 INFO @ Tue, 14 Jul 2020 07:07:41: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:07:46: 8000000 INFO @ Tue, 14 Jul 2020 07:07:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262193/SRX7262193.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:07:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262193/SRX7262193.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:07:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262193/SRX7262193.10_summits.bed INFO @ Tue, 14 Jul 2020 07:07:50: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (470 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:07:52: 9000000 INFO @ Tue, 14 Jul 2020 07:07:52: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:07:52: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:07:52: #1 total tags in treatment: 9031123 INFO @ Tue, 14 Jul 2020 07:07:52: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:07:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:07:53: #1 tags after filtering in treatment: 9031123 INFO @ Tue, 14 Jul 2020 07:07:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:07:53: #1 finished! INFO @ Tue, 14 Jul 2020 07:07:53: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:07:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:07:53: #2 number of paired peaks: 402 WARNING @ Tue, 14 Jul 2020 07:07:53: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Tue, 14 Jul 2020 07:07:53: start model_add_line... INFO @ Tue, 14 Jul 2020 07:07:53: start X-correlation... INFO @ Tue, 14 Jul 2020 07:07:53: end of X-cor INFO @ Tue, 14 Jul 2020 07:07:53: #2 finished! INFO @ Tue, 14 Jul 2020 07:07:53: #2 predicted fragment length is 46 bps INFO @ Tue, 14 Jul 2020 07:07:53: #2 alternative fragment length(s) may be 2,46,542 bps INFO @ Tue, 14 Jul 2020 07:07:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262193/SRX7262193.20_model.r WARNING @ Tue, 14 Jul 2020 07:07:53: #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, 14 Jul 2020 07:07:53: #2 You may need to consider one of the other alternative d(s): 2,46,542 WARNING @ Tue, 14 Jul 2020 07:07:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:07:53: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:07:53: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:08:10: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:08:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262193/SRX7262193.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:08:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262193/SRX7262193.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:08:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262193/SRX7262193.20_summits.bed INFO @ Tue, 14 Jul 2020 07:08:19: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (176 records, 4 fields): 22 millis CompletedMACS2peakCalling