Job ID = 6367767 SRX = SRX4082381 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:42:14 prefetch.2.10.7: 1) Downloading 'SRR7164199'... 2020-06-15T23:42:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:43:30 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:43:31 prefetch.2.10.7: 'SRR7164199' is valid 2020-06-15T23:43:31 prefetch.2.10.7: 1) 'SRR7164199' was downloaded successfully 2020-06-15T23:43:31 prefetch.2.10.7: 'SRR7164199' has 0 unresolved dependencies Read 12919188 spots for SRR7164199/SRR7164199.sra Written 12919188 spots for SRR7164199/SRR7164199.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: 00:02:45 12919188 reads; of these: 12919188 (100.00%) were unpaired; of these: 1421032 (11.00%) aligned 0 times 8807742 (68.18%) aligned exactly 1 time 2690414 (20.82%) aligned >1 times 89.00% overall alignment rate Time searching: 00:02:45 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] 4815656 / 11498156 = 0.4188 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 08:49:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082381/SRX4082381.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082381/SRX4082381.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082381/SRX4082381.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082381/SRX4082381.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 08:49:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:37: 1000000 INFO @ Tue, 16 Jun 2020 08:49:43: 2000000 INFO @ Tue, 16 Jun 2020 08:49:49: 3000000 INFO @ Tue, 16 Jun 2020 08:49:55: 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, 16 Jun 2020 08:50:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082381/SRX4082381.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082381/SRX4082381.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082381/SRX4082381.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082381/SRX4082381.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 08:50:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:50:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:50:02: 5000000 INFO @ Tue, 16 Jun 2020 08:50:06: 1000000 INFO @ Tue, 16 Jun 2020 08:50:08: 6000000 INFO @ Tue, 16 Jun 2020 08:50:12: 2000000 INFO @ Tue, 16 Jun 2020 08:50:12: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:50:12: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:50:12: #1 total tags in treatment: 6682500 INFO @ Tue, 16 Jun 2020 08:50:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:12: #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 08:50:13: #1 tags after filtering in treatment: 6682500 INFO @ Tue, 16 Jun 2020 08:50:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:13: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:13: #2 number of paired peaks: 652 WARNING @ Tue, 16 Jun 2020 08:50:13: Fewer paired peaks (652) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 652 pairs to build model! INFO @ Tue, 16 Jun 2020 08:50:13: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:13: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:13: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:13: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:13: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:50:13: #2 alternative fragment length(s) may be 3,49 bps INFO @ Tue, 16 Jun 2020 08:50:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082381/SRX4082381.05_model.r WARNING @ Tue, 16 Jun 2020 08:50:13: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:50:13: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Tue, 16 Jun 2020 08:50:13: #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 08:50:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:50:18: 3000000 INFO @ Tue, 16 Jun 2020 08:50:23: 4000000 INFO @ Tue, 16 Jun 2020 08:50:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:50:28: 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 08:50:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082381/SRX4082381.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082381/SRX4082381.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082381/SRX4082381.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082381/SRX4082381.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 08:50:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:50:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:50:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082381/SRX4082381.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:50:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082381/SRX4082381.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:50:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082381/SRX4082381.05_summits.bed INFO @ Tue, 16 Jun 2020 08:50:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (816 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:50:34: 6000000 INFO @ Tue, 16 Jun 2020 08:50:38: 1000000 INFO @ Tue, 16 Jun 2020 08:50:38: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:50:38: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:50:38: #1 total tags in treatment: 6682500 INFO @ Tue, 16 Jun 2020 08:50:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:38: #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 08:50:38: #1 tags after filtering in treatment: 6682500 INFO @ Tue, 16 Jun 2020 08:50:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:39: #2 number of paired peaks: 652 WARNING @ Tue, 16 Jun 2020 08:50:39: Fewer paired peaks (652) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 652 pairs to build model! INFO @ Tue, 16 Jun 2020 08:50:39: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:39: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:39: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:39: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:39: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:50:39: #2 alternative fragment length(s) may be 3,49 bps INFO @ Tue, 16 Jun 2020 08:50:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082381/SRX4082381.10_model.r WARNING @ Tue, 16 Jun 2020 08:50:39: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:50:39: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Tue, 16 Jun 2020 08:50:39: #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 08:50:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:50:44: 2000000 INFO @ Tue, 16 Jun 2020 08:50:50: 3000000 INFO @ Tue, 16 Jun 2020 08:50:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:50:56: 4000000 INFO @ Tue, 16 Jun 2020 08:50:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082381/SRX4082381.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:50:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082381/SRX4082381.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:50:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082381/SRX4082381.10_summits.bed INFO @ Tue, 16 Jun 2020 08:50:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (475 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:51:02: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:51:09: 6000000 INFO @ Tue, 16 Jun 2020 08:51:13: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:51:13: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:51:13: #1 total tags in treatment: 6682500 INFO @ Tue, 16 Jun 2020 08:51:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:51:13: #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 08:51:13: #1 tags after filtering in treatment: 6682500 INFO @ Tue, 16 Jun 2020 08:51:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:51:13: #1 finished! INFO @ Tue, 16 Jun 2020 08:51:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:51:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:51:14: #2 number of paired peaks: 652 WARNING @ Tue, 16 Jun 2020 08:51:14: Fewer paired peaks (652) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 652 pairs to build model! INFO @ Tue, 16 Jun 2020 08:51:14: start model_add_line... INFO @ Tue, 16 Jun 2020 08:51:14: start X-correlation... INFO @ Tue, 16 Jun 2020 08:51:14: end of X-cor INFO @ Tue, 16 Jun 2020 08:51:14: #2 finished! INFO @ Tue, 16 Jun 2020 08:51:14: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:51:14: #2 alternative fragment length(s) may be 3,49 bps INFO @ Tue, 16 Jun 2020 08:51:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082381/SRX4082381.20_model.r WARNING @ Tue, 16 Jun 2020 08:51:14: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:51:14: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Tue, 16 Jun 2020 08:51:14: #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 08:51:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:51:14: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:51:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:51:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082381/SRX4082381.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:51:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082381/SRX4082381.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:51:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082381/SRX4082381.20_summits.bed INFO @ Tue, 16 Jun 2020 08:51:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (223 records, 4 fields): 1 millis CompletedMACS2peakCalling