Job ID = 6366649 SRX = SRX2163950 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:54:44 prefetch.2.10.7: 1) Downloading 'SRR4242865'... 2020-06-15T22:54:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:01:45 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:01:45 prefetch.2.10.7: 1) 'SRR4242865' was downloaded successfully Read 50549812 spots for SRR4242865/SRR4242865.sra Written 50549812 spots for SRR4242865/SRR4242865.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: 00:18:33 50549812 reads; of these: 50549812 (100.00%) were unpaired; of these: 9218569 (18.24%) aligned 0 times 36282722 (71.78%) aligned exactly 1 time 5048521 (9.99%) aligned >1 times 81.76% overall alignment rate Time searching: 00:18:33 Overall time: 00:18:33 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 20 files... [bam_rmdupse_core] 18170474 / 41331243 = 0.4396 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 08:36:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2163950/SRX2163950.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2163950/SRX2163950.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2163950/SRX2163950.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2163950/SRX2163950.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 08:36:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:36:44: 1000000 INFO @ Tue, 16 Jun 2020 08:36:53: 2000000 INFO @ Tue, 16 Jun 2020 08:37:02: 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 08:37:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2163950/SRX2163950.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2163950/SRX2163950.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2163950/SRX2163950.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2163950/SRX2163950.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 08:37:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:37:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:37:11: 4000000 INFO @ Tue, 16 Jun 2020 08:37:16: 1000000 INFO @ Tue, 16 Jun 2020 08:37:22: 5000000 INFO @ Tue, 16 Jun 2020 08:37:26: 2000000 INFO @ Tue, 16 Jun 2020 08:37:32: 6000000 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 08:37:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2163950/SRX2163950.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2163950/SRX2163950.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2163950/SRX2163950.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2163950/SRX2163950.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 08:37:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:37:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:37:36: 3000000 INFO @ Tue, 16 Jun 2020 08:37:42: 7000000 INFO @ Tue, 16 Jun 2020 08:37:46: 4000000 INFO @ Tue, 16 Jun 2020 08:37:46: 1000000 INFO @ Tue, 16 Jun 2020 08:37:53: 8000000 INFO @ Tue, 16 Jun 2020 08:37:56: 5000000 INFO @ Tue, 16 Jun 2020 08:37:57: 2000000 INFO @ Tue, 16 Jun 2020 08:38:03: 9000000 INFO @ Tue, 16 Jun 2020 08:38:06: 6000000 INFO @ Tue, 16 Jun 2020 08:38:07: 3000000 INFO @ Tue, 16 Jun 2020 08:38:13: 10000000 INFO @ Tue, 16 Jun 2020 08:38:16: 7000000 INFO @ Tue, 16 Jun 2020 08:38:17: 4000000 INFO @ Tue, 16 Jun 2020 08:38:23: 11000000 INFO @ Tue, 16 Jun 2020 08:38:26: 8000000 INFO @ Tue, 16 Jun 2020 08:38:28: 5000000 INFO @ Tue, 16 Jun 2020 08:38:34: 12000000 INFO @ Tue, 16 Jun 2020 08:38:36: 9000000 INFO @ Tue, 16 Jun 2020 08:38:38: 6000000 INFO @ Tue, 16 Jun 2020 08:38:44: 13000000 INFO @ Tue, 16 Jun 2020 08:38:46: 10000000 INFO @ Tue, 16 Jun 2020 08:38:49: 7000000 INFO @ Tue, 16 Jun 2020 08:38:55: 14000000 INFO @ Tue, 16 Jun 2020 08:38:57: 11000000 INFO @ Tue, 16 Jun 2020 08:38:59: 8000000 INFO @ Tue, 16 Jun 2020 08:39:05: 15000000 INFO @ Tue, 16 Jun 2020 08:39:07: 12000000 INFO @ Tue, 16 Jun 2020 08:39:10: 9000000 INFO @ Tue, 16 Jun 2020 08:39:15: 16000000 INFO @ Tue, 16 Jun 2020 08:39:17: 13000000 INFO @ Tue, 16 Jun 2020 08:39:20: 10000000 INFO @ Tue, 16 Jun 2020 08:39:26: 17000000 INFO @ Tue, 16 Jun 2020 08:39:27: 14000000 INFO @ Tue, 16 Jun 2020 08:39:31: 11000000 INFO @ Tue, 16 Jun 2020 08:39:36: 18000000 INFO @ Tue, 16 Jun 2020 08:39:37: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:39:42: 12000000 INFO @ Tue, 16 Jun 2020 08:39:47: 19000000 INFO @ Tue, 16 Jun 2020 08:39:47: 16000000 INFO @ Tue, 16 Jun 2020 08:39:52: 13000000 INFO @ Tue, 16 Jun 2020 08:39:57: 20000000 INFO @ Tue, 16 Jun 2020 08:39:57: 17000000 INFO @ Tue, 16 Jun 2020 08:40:03: 14000000 INFO @ Tue, 16 Jun 2020 08:40:07: 21000000 INFO @ Tue, 16 Jun 2020 08:40:08: 18000000 INFO @ Tue, 16 Jun 2020 08:40:13: 15000000 INFO @ Tue, 16 Jun 2020 08:40:18: 22000000 INFO @ Tue, 16 Jun 2020 08:40:18: 19000000 INFO @ Tue, 16 Jun 2020 08:40:24: 16000000 INFO @ Tue, 16 Jun 2020 08:40:28: 23000000 INFO @ Tue, 16 Jun 2020 08:40:28: 20000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:40:30: #1 tag size is determined as 92 bps INFO @ Tue, 16 Jun 2020 08:40:30: #1 tag size = 92 INFO @ Tue, 16 Jun 2020 08:40:30: #1 total tags in treatment: 23160769 INFO @ Tue, 16 Jun 2020 08:40:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:40:30: #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 08:40:30: #1 tags after filtering in treatment: 23160769 INFO @ Tue, 16 Jun 2020 08:40:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:40:30: #1 finished! INFO @ Tue, 16 Jun 2020 08:40:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:40:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:40:32: #2 number of paired peaks: 351 WARNING @ Tue, 16 Jun 2020 08:40:32: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Tue, 16 Jun 2020 08:40:32: start model_add_line... INFO @ Tue, 16 Jun 2020 08:40:32: start X-correlation... INFO @ Tue, 16 Jun 2020 08:40:32: end of X-cor INFO @ Tue, 16 Jun 2020 08:40:32: #2 finished! INFO @ Tue, 16 Jun 2020 08:40:32: #2 predicted fragment length is 128 bps INFO @ Tue, 16 Jun 2020 08:40:32: #2 alternative fragment length(s) may be 3,128 bps INFO @ Tue, 16 Jun 2020 08:40:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2163950/SRX2163950.05_model.r WARNING @ Tue, 16 Jun 2020 08:40:32: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:40:32: #2 You may need to consider one of the other alternative d(s): 3,128 WARNING @ Tue, 16 Jun 2020 08:40:32: #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 08:40:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:40:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:40:34: 17000000 INFO @ Tue, 16 Jun 2020 08:40:38: 21000000 INFO @ Tue, 16 Jun 2020 08:40:45: 18000000 INFO @ Tue, 16 Jun 2020 08:40:48: 22000000 INFO @ Tue, 16 Jun 2020 08:40:55: 19000000 INFO @ Tue, 16 Jun 2020 08:40:58: 23000000 INFO @ Tue, 16 Jun 2020 08:41:00: #1 tag size is determined as 92 bps INFO @ Tue, 16 Jun 2020 08:41:00: #1 tag size = 92 INFO @ Tue, 16 Jun 2020 08:41:00: #1 total tags in treatment: 23160769 INFO @ Tue, 16 Jun 2020 08:41:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:41:00: #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 08:41:00: #1 tags after filtering in treatment: 23160769 INFO @ Tue, 16 Jun 2020 08:41:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:41:00: #1 finished! INFO @ Tue, 16 Jun 2020 08:41:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:41:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:41:02: #2 number of paired peaks: 351 WARNING @ Tue, 16 Jun 2020 08:41:02: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Tue, 16 Jun 2020 08:41:02: start model_add_line... INFO @ Tue, 16 Jun 2020 08:41:02: start X-correlation... INFO @ Tue, 16 Jun 2020 08:41:02: end of X-cor INFO @ Tue, 16 Jun 2020 08:41:02: #2 finished! INFO @ Tue, 16 Jun 2020 08:41:02: #2 predicted fragment length is 128 bps INFO @ Tue, 16 Jun 2020 08:41:02: #2 alternative fragment length(s) may be 3,128 bps INFO @ Tue, 16 Jun 2020 08:41:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2163950/SRX2163950.10_model.r WARNING @ Tue, 16 Jun 2020 08:41:02: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:41:02: #2 You may need to consider one of the other alternative d(s): 3,128 WARNING @ Tue, 16 Jun 2020 08:41:02: #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 08:41:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:41:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:41:05: 20000000 INFO @ Tue, 16 Jun 2020 08:41:14: 21000000 INFO @ Tue, 16 Jun 2020 08:41:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:41:21: 22000000 INFO @ Tue, 16 Jun 2020 08:41:28: 23000000 INFO @ Tue, 16 Jun 2020 08:41:29: #1 tag size is determined as 92 bps INFO @ Tue, 16 Jun 2020 08:41:29: #1 tag size = 92 INFO @ Tue, 16 Jun 2020 08:41:29: #1 total tags in treatment: 23160769 INFO @ Tue, 16 Jun 2020 08:41:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:41:29: #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 08:41:30: #1 tags after filtering in treatment: 23160769 INFO @ Tue, 16 Jun 2020 08:41:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:41:30: #1 finished! INFO @ Tue, 16 Jun 2020 08:41:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:41:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:41:31: #2 number of paired peaks: 351 WARNING @ Tue, 16 Jun 2020 08:41:31: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Tue, 16 Jun 2020 08:41:31: start model_add_line... INFO @ Tue, 16 Jun 2020 08:41:31: start X-correlation... INFO @ Tue, 16 Jun 2020 08:41:31: end of X-cor INFO @ Tue, 16 Jun 2020 08:41:31: #2 finished! INFO @ Tue, 16 Jun 2020 08:41:31: #2 predicted fragment length is 128 bps INFO @ Tue, 16 Jun 2020 08:41:31: #2 alternative fragment length(s) may be 3,128 bps INFO @ Tue, 16 Jun 2020 08:41:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2163950/SRX2163950.20_model.r WARNING @ Tue, 16 Jun 2020 08:41:31: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:41:31: #2 You may need to consider one of the other alternative d(s): 3,128 WARNING @ Tue, 16 Jun 2020 08:41:31: #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 08:41:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:41:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:41:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2163950/SRX2163950.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:41:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2163950/SRX2163950.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:41:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2163950/SRX2163950.05_summits.bed INFO @ Tue, 16 Jun 2020 08:41:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6645 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:41:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:42:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2163950/SRX2163950.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:42:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2163950/SRX2163950.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:42:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2163950/SRX2163950.10_summits.bed INFO @ Tue, 16 Jun 2020 08:42:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4507 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:42:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:42:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2163950/SRX2163950.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:42:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2163950/SRX2163950.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:42:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2163950/SRX2163950.20_summits.bed INFO @ Tue, 16 Jun 2020 08:42:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2655 records, 4 fields): 3 millis CompletedMACS2peakCalling