Job ID = 6368521 SRX = SRX5020750 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:13:20 prefetch.2.10.7: 1) Downloading 'SRR8201373'... 2020-06-16T00:13:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:16:41 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:16:41 prefetch.2.10.7: 1) 'SRR8201373' was downloaded successfully 2020-06-16T00:16:41 prefetch.2.10.7: 'SRR8201373' has 0 unresolved dependencies Read 27817518 spots for SRR8201373/SRR8201373.sra Written 27817518 spots for SRR8201373/SRR8201373.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: 00:08:52 27817518 reads; of these: 27817518 (100.00%) were unpaired; of these: 1147079 (4.12%) aligned 0 times 22203151 (79.82%) aligned exactly 1 time 4467288 (16.06%) aligned >1 times 95.88% overall alignment rate Time searching: 00:08:52 Overall time: 00:08:52 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] 4865421 / 26670439 = 0.1824 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 09:33:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020750/SRX5020750.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020750/SRX5020750.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020750/SRX5020750.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020750/SRX5020750.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 09:33:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:33:50: 1000000 INFO @ Tue, 16 Jun 2020 09:33:56: 2000000 INFO @ Tue, 16 Jun 2020 09:34:02: 3000000 INFO @ Tue, 16 Jun 2020 09:34:09: 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 09:34:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020750/SRX5020750.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020750/SRX5020750.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020750/SRX5020750.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020750/SRX5020750.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 09:34:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:15: 5000000 INFO @ Tue, 16 Jun 2020 09:34:21: 1000000 INFO @ Tue, 16 Jun 2020 09:34:23: 6000000 INFO @ Tue, 16 Jun 2020 09:34:30: 7000000 INFO @ Tue, 16 Jun 2020 09:34:30: 2000000 INFO @ Tue, 16 Jun 2020 09:34:37: 8000000 INFO @ Tue, 16 Jun 2020 09:34:39: 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 09:34:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020750/SRX5020750.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020750/SRX5020750.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020750/SRX5020750.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020750/SRX5020750.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 09:34:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:45: 9000000 INFO @ Tue, 16 Jun 2020 09:34:47: 4000000 INFO @ Tue, 16 Jun 2020 09:34:51: 1000000 INFO @ Tue, 16 Jun 2020 09:34:53: 10000000 INFO @ Tue, 16 Jun 2020 09:34:56: 5000000 INFO @ Tue, 16 Jun 2020 09:35:00: 2000000 INFO @ Tue, 16 Jun 2020 09:35:00: 11000000 INFO @ Tue, 16 Jun 2020 09:35:04: 6000000 INFO @ Tue, 16 Jun 2020 09:35:08: 12000000 INFO @ Tue, 16 Jun 2020 09:35:09: 3000000 INFO @ Tue, 16 Jun 2020 09:35:13: 7000000 INFO @ Tue, 16 Jun 2020 09:35:16: 13000000 INFO @ Tue, 16 Jun 2020 09:35:18: 4000000 INFO @ Tue, 16 Jun 2020 09:35:22: 8000000 INFO @ Tue, 16 Jun 2020 09:35:23: 14000000 INFO @ Tue, 16 Jun 2020 09:35:26: 5000000 INFO @ Tue, 16 Jun 2020 09:35:30: 9000000 INFO @ Tue, 16 Jun 2020 09:35:31: 15000000 INFO @ Tue, 16 Jun 2020 09:35:35: 6000000 INFO @ Tue, 16 Jun 2020 09:35:39: 16000000 INFO @ Tue, 16 Jun 2020 09:35:39: 10000000 INFO @ Tue, 16 Jun 2020 09:35:43: 7000000 INFO @ Tue, 16 Jun 2020 09:35:46: 17000000 INFO @ Tue, 16 Jun 2020 09:35:47: 11000000 INFO @ Tue, 16 Jun 2020 09:35:52: 8000000 INFO @ Tue, 16 Jun 2020 09:35:54: 18000000 INFO @ Tue, 16 Jun 2020 09:35:56: 12000000 INFO @ Tue, 16 Jun 2020 09:36:00: 9000000 INFO @ Tue, 16 Jun 2020 09:36:02: 19000000 INFO @ Tue, 16 Jun 2020 09:36:04: 13000000 INFO @ Tue, 16 Jun 2020 09:36:09: 10000000 INFO @ Tue, 16 Jun 2020 09:36:09: 20000000 INFO @ Tue, 16 Jun 2020 09:36:13: 14000000 INFO @ Tue, 16 Jun 2020 09:36:17: 21000000 INFO @ Tue, 16 Jun 2020 09:36:17: 11000000 INFO @ Tue, 16 Jun 2020 09:36:21: 15000000 INFO @ Tue, 16 Jun 2020 09:36:23: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:36:23: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:36:23: #1 total tags in treatment: 21805018 INFO @ Tue, 16 Jun 2020 09:36:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:36:23: #1 tags after filtering in treatment: 21805018 INFO @ Tue, 16 Jun 2020 09:36:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:36:23: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:25: #2 number of paired peaks: 184 WARNING @ Tue, 16 Jun 2020 09:36:25: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Tue, 16 Jun 2020 09:36:25: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:25: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:25: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:25: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:25: #2 predicted fragment length is 63 bps INFO @ Tue, 16 Jun 2020 09:36:25: #2 alternative fragment length(s) may be 2,63 bps INFO @ Tue, 16 Jun 2020 09:36:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020750/SRX5020750.05_model.r WARNING @ Tue, 16 Jun 2020 09:36:25: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:36:25: #2 You may need to consider one of the other alternative d(s): 2,63 WARNING @ Tue, 16 Jun 2020 09:36:25: #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 09:36:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:36:26: 12000000 INFO @ Tue, 16 Jun 2020 09:36:30: 16000000 INFO @ Tue, 16 Jun 2020 09:36:34: 13000000 INFO @ Tue, 16 Jun 2020 09:36:38: 17000000 INFO @ Tue, 16 Jun 2020 09:36:43: 14000000 INFO @ Tue, 16 Jun 2020 09:36:47: 18000000 INFO @ Tue, 16 Jun 2020 09:36:51: 15000000 INFO @ Tue, 16 Jun 2020 09:36:55: 19000000 INFO @ Tue, 16 Jun 2020 09:36:59: 16000000 INFO @ Tue, 16 Jun 2020 09:37:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:37:04: 20000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:37:08: 17000000 INFO @ Tue, 16 Jun 2020 09:37:12: 21000000 INFO @ Tue, 16 Jun 2020 09:37:16: 18000000 INFO @ Tue, 16 Jun 2020 09:37:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020750/SRX5020750.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:37:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020750/SRX5020750.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:37:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020750/SRX5020750.05_summits.bed INFO @ Tue, 16 Jun 2020 09:37:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5630 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:37:19: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:37:19: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:37:19: #1 total tags in treatment: 21805018 INFO @ Tue, 16 Jun 2020 09:37:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:37:19: #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 09:37:19: #1 tags after filtering in treatment: 21805018 INFO @ Tue, 16 Jun 2020 09:37:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:37:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:37:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:37:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:37:21: #2 number of paired peaks: 184 WARNING @ Tue, 16 Jun 2020 09:37:21: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Tue, 16 Jun 2020 09:37:21: start model_add_line... INFO @ Tue, 16 Jun 2020 09:37:21: start X-correlation... INFO @ Tue, 16 Jun 2020 09:37:21: end of X-cor INFO @ Tue, 16 Jun 2020 09:37:21: #2 finished! INFO @ Tue, 16 Jun 2020 09:37:21: #2 predicted fragment length is 63 bps INFO @ Tue, 16 Jun 2020 09:37:21: #2 alternative fragment length(s) may be 2,63 bps INFO @ Tue, 16 Jun 2020 09:37:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020750/SRX5020750.10_model.r WARNING @ Tue, 16 Jun 2020 09:37:21: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:37:21: #2 You may need to consider one of the other alternative d(s): 2,63 WARNING @ Tue, 16 Jun 2020 09:37:21: #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 09:37:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:37:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:37:24: 19000000 INFO @ Tue, 16 Jun 2020 09:37:32: 20000000 INFO @ Tue, 16 Jun 2020 09:37:40: 21000000 INFO @ Tue, 16 Jun 2020 09:37:46: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:37:46: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:37:46: #1 total tags in treatment: 21805018 INFO @ Tue, 16 Jun 2020 09:37:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:37:46: #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 09:37:46: #1 tags after filtering in treatment: 21805018 INFO @ Tue, 16 Jun 2020 09:37:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:37:46: #1 finished! INFO @ Tue, 16 Jun 2020 09:37:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:37:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:37:47: #2 number of paired peaks: 184 WARNING @ Tue, 16 Jun 2020 09:37:47: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Tue, 16 Jun 2020 09:37:47: start model_add_line... INFO @ Tue, 16 Jun 2020 09:37:48: start X-correlation... INFO @ Tue, 16 Jun 2020 09:37:48: end of X-cor INFO @ Tue, 16 Jun 2020 09:37:48: #2 finished! INFO @ Tue, 16 Jun 2020 09:37:48: #2 predicted fragment length is 63 bps INFO @ Tue, 16 Jun 2020 09:37:48: #2 alternative fragment length(s) may be 2,63 bps INFO @ Tue, 16 Jun 2020 09:37:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020750/SRX5020750.20_model.r WARNING @ Tue, 16 Jun 2020 09:37:48: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:37:48: #2 You may need to consider one of the other alternative d(s): 2,63 WARNING @ Tue, 16 Jun 2020 09:37:48: #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 09:37:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:37:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:37:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:38:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020750/SRX5020750.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:38:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020750/SRX5020750.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:38:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020750/SRX5020750.10_summits.bed INFO @ Tue, 16 Jun 2020 09:38:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1428 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:38:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:38:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020750/SRX5020750.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:38:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020750/SRX5020750.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:38:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020750/SRX5020750.20_summits.bed INFO @ Tue, 16 Jun 2020 09:38:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (262 records, 4 fields): 1 millis CompletedMACS2peakCalling