Job ID = 6367905 SRX = SRX4194198 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:44:18 prefetch.2.10.7: 1) Downloading 'SRR7291479'... 2020-06-15T23:44:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:45:24 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:45:25 prefetch.2.10.7: 'SRR7291479' is valid 2020-06-15T23:45:25 prefetch.2.10.7: 1) 'SRR7291479' was downloaded successfully 2020-06-15T23:45:25 prefetch.2.10.7: 'SRR7291479' has 0 unresolved dependencies Read 6427827 spots for SRR7291479/SRR7291479.sra Written 6427827 spots for SRR7291479/SRR7291479.sra 2020-06-15T23:45:58 prefetch.2.10.7: 1) Downloading 'SRR7291480'... 2020-06-15T23:45:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:47:31 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:47:31 prefetch.2.10.7: 'SRR7291480' is valid 2020-06-15T23:47:31 prefetch.2.10.7: 1) 'SRR7291480' was downloaded successfully 2020-06-15T23:47:31 prefetch.2.10.7: 'SRR7291480' has 0 unresolved dependencies Read 6256271 spots for SRR7291480/SRR7291480.sra Written 6256271 spots for SRR7291480/SRR7291480.sra 2020-06-15T23:48:04 prefetch.2.10.7: 1) Downloading 'SRR7291481'... 2020-06-15T23:48:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:49:35 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:49:35 prefetch.2.10.7: 'SRR7291481' is valid 2020-06-15T23:49:35 prefetch.2.10.7: 1) 'SRR7291481' was downloaded successfully 2020-06-15T23:49:35 prefetch.2.10.7: 'SRR7291481' has 0 unresolved dependencies Read 6450099 spots for SRR7291481/SRR7291481.sra Written 6450099 spots for SRR7291481/SRR7291481.sra 2020-06-15T23:50:09 prefetch.2.10.7: 1) Downloading 'SRR7291482'... 2020-06-15T23:50:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:51:02 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:51:02 prefetch.2.10.7: 'SRR7291482' is valid 2020-06-15T23:51:02 prefetch.2.10.7: 1) 'SRR7291482' was downloaded successfully 2020-06-15T23:51:02 prefetch.2.10.7: 'SRR7291482' has 0 unresolved dependencies Read 6218328 spots for SRR7291482/SRR7291482.sra Written 6218328 spots for SRR7291482/SRR7291482.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: 00:10:09 25352525 reads; of these: 25352525 (100.00%) were unpaired; of these: 591307 (2.33%) aligned 0 times 20124148 (79.38%) aligned exactly 1 time 4637070 (18.29%) aligned >1 times 97.67% overall alignment rate Time searching: 00:10:09 Overall time: 00:10:09 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 12 files... [bam_rmdupse_core] 11263024 / 24761218 = 0.4549 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 09:08:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194198/SRX4194198.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194198/SRX4194198.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194198/SRX4194198.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194198/SRX4194198.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 09:08:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:08:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:08:43: 1000000 INFO @ Tue, 16 Jun 2020 09:08:51: 2000000 INFO @ Tue, 16 Jun 2020 09:08:58: 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 @ Tue, 16 Jun 2020 09:09:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194198/SRX4194198.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194198/SRX4194198.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194198/SRX4194198.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194198/SRX4194198.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 09:09:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:05: 4000000 INFO @ Tue, 16 Jun 2020 09:09:14: 5000000 INFO @ Tue, 16 Jun 2020 09:09:14: 1000000 INFO @ Tue, 16 Jun 2020 09:09:22: 6000000 INFO @ Tue, 16 Jun 2020 09:09:22: 2000000 INFO @ Tue, 16 Jun 2020 09:09:29: 7000000 INFO @ Tue, 16 Jun 2020 09:09:30: 3000000 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 09:09:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194198/SRX4194198.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194198/SRX4194198.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194198/SRX4194198.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194198/SRX4194198.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 09:09:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:38: 4000000 INFO @ Tue, 16 Jun 2020 09:09:38: 8000000 INFO @ Tue, 16 Jun 2020 09:09:44: 1000000 INFO @ Tue, 16 Jun 2020 09:09:46: 9000000 INFO @ Tue, 16 Jun 2020 09:09:46: 5000000 INFO @ Tue, 16 Jun 2020 09:09:52: 2000000 INFO @ Tue, 16 Jun 2020 09:09:54: 10000000 INFO @ Tue, 16 Jun 2020 09:09:54: 6000000 INFO @ Tue, 16 Jun 2020 09:10:00: 3000000 INFO @ Tue, 16 Jun 2020 09:10:01: 11000000 INFO @ Tue, 16 Jun 2020 09:10:02: 7000000 INFO @ Tue, 16 Jun 2020 09:10:08: 4000000 INFO @ Tue, 16 Jun 2020 09:10:09: 12000000 INFO @ Tue, 16 Jun 2020 09:10:10: 8000000 INFO @ Tue, 16 Jun 2020 09:10:16: 5000000 INFO @ Tue, 16 Jun 2020 09:10:17: 13000000 INFO @ Tue, 16 Jun 2020 09:10:18: 9000000 INFO @ Tue, 16 Jun 2020 09:10:21: #1 tag size is determined as 57 bps INFO @ Tue, 16 Jun 2020 09:10:21: #1 tag size = 57 INFO @ Tue, 16 Jun 2020 09:10:21: #1 total tags in treatment: 13498194 INFO @ Tue, 16 Jun 2020 09:10:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:10:21: #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 09:10:22: #1 tags after filtering in treatment: 13498194 INFO @ Tue, 16 Jun 2020 09:10:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:10:22: #1 finished! INFO @ Tue, 16 Jun 2020 09:10:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:10:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:10:23: #2 number of paired peaks: 482 WARNING @ Tue, 16 Jun 2020 09:10:23: Fewer paired peaks (482) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 482 pairs to build model! INFO @ Tue, 16 Jun 2020 09:10:23: start model_add_line... INFO @ Tue, 16 Jun 2020 09:10:23: start X-correlation... INFO @ Tue, 16 Jun 2020 09:10:23: end of X-cor INFO @ Tue, 16 Jun 2020 09:10:23: #2 finished! INFO @ Tue, 16 Jun 2020 09:10:23: #2 predicted fragment length is 67 bps INFO @ Tue, 16 Jun 2020 09:10:23: #2 alternative fragment length(s) may be 4,67 bps INFO @ Tue, 16 Jun 2020 09:10:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194198/SRX4194198.05_model.r WARNING @ Tue, 16 Jun 2020 09:10:23: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:10:23: #2 You may need to consider one of the other alternative d(s): 4,67 WARNING @ Tue, 16 Jun 2020 09:10:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:10:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:10:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:10:24: 6000000 INFO @ Tue, 16 Jun 2020 09:10:26: 10000000 INFO @ Tue, 16 Jun 2020 09:10:32: 7000000 INFO @ Tue, 16 Jun 2020 09:10:34: 11000000 INFO @ Tue, 16 Jun 2020 09:10:40: 8000000 INFO @ Tue, 16 Jun 2020 09:10:42: 12000000 INFO @ Tue, 16 Jun 2020 09:10:48: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:10:49: 13000000 INFO @ Tue, 16 Jun 2020 09:10:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:10:53: #1 tag size is determined as 57 bps INFO @ Tue, 16 Jun 2020 09:10:53: #1 tag size = 57 INFO @ Tue, 16 Jun 2020 09:10:53: #1 total tags in treatment: 13498194 INFO @ Tue, 16 Jun 2020 09:10:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:10:53: #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 09:10:54: #1 tags after filtering in treatment: 13498194 INFO @ Tue, 16 Jun 2020 09:10:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:10:54: #1 finished! INFO @ Tue, 16 Jun 2020 09:10:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:10:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:10:55: #2 number of paired peaks: 482 WARNING @ Tue, 16 Jun 2020 09:10:55: Fewer paired peaks (482) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 482 pairs to build model! INFO @ Tue, 16 Jun 2020 09:10:55: start model_add_line... INFO @ Tue, 16 Jun 2020 09:10:55: start X-correlation... INFO @ Tue, 16 Jun 2020 09:10:55: end of X-cor INFO @ Tue, 16 Jun 2020 09:10:55: #2 finished! INFO @ Tue, 16 Jun 2020 09:10:55: #2 predicted fragment length is 67 bps INFO @ Tue, 16 Jun 2020 09:10:55: #2 alternative fragment length(s) may be 4,67 bps INFO @ Tue, 16 Jun 2020 09:10:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194198/SRX4194198.10_model.r WARNING @ Tue, 16 Jun 2020 09:10:55: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:10:55: #2 You may need to consider one of the other alternative d(s): 4,67 WARNING @ Tue, 16 Jun 2020 09:10:55: #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 09:10:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:10:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:10:55: 10000000 INFO @ Tue, 16 Jun 2020 09:11:03: 11000000 INFO @ Tue, 16 Jun 2020 09:11:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194198/SRX4194198.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194198/SRX4194198.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194198/SRX4194198.05_summits.bed INFO @ Tue, 16 Jun 2020 09:11:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1579 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:11:10: 12000000 INFO @ Tue, 16 Jun 2020 09:11:17: 13000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:11:21: #1 tag size is determined as 57 bps INFO @ Tue, 16 Jun 2020 09:11:21: #1 tag size = 57 INFO @ Tue, 16 Jun 2020 09:11:21: #1 total tags in treatment: 13498194 INFO @ Tue, 16 Jun 2020 09:11:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:21: #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 09:11:21: #1 tags after filtering in treatment: 13498194 INFO @ Tue, 16 Jun 2020 09:11:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:11:21: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:22: #2 number of paired peaks: 482 WARNING @ Tue, 16 Jun 2020 09:11:22: Fewer paired peaks (482) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 482 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:22: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:22: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:22: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:22: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:22: #2 predicted fragment length is 67 bps INFO @ Tue, 16 Jun 2020 09:11:22: #2 alternative fragment length(s) may be 4,67 bps INFO @ Tue, 16 Jun 2020 09:11:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194198/SRX4194198.20_model.r WARNING @ Tue, 16 Jun 2020 09:11:22: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:11:22: #2 You may need to consider one of the other alternative d(s): 4,67 WARNING @ Tue, 16 Jun 2020 09:11:22: #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 09:11:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:11:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:11:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194198/SRX4194198.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194198/SRX4194198.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194198/SRX4194198.10_summits.bed INFO @ Tue, 16 Jun 2020 09:11:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (830 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:11:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194198/SRX4194198.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194198/SRX4194198.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194198/SRX4194198.20_summits.bed INFO @ Tue, 16 Jun 2020 09:12:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (414 records, 4 fields): 1 millis CompletedMACS2peakCalling