Job ID = 6368541 SRX = SRX5020769 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:21:21 prefetch.2.10.7: 1) Downloading 'SRR8201392'... 2020-06-16T00:21:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:23:39 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:23:40 prefetch.2.10.7: 'SRR8201392' is valid 2020-06-16T00:23:40 prefetch.2.10.7: 1) 'SRR8201392' was downloaded successfully 2020-06-16T00:23:40 prefetch.2.10.7: 'SRR8201392' has 0 unresolved dependencies Read 18036313 spots for SRR8201392/SRR8201392.sra Written 18036313 spots for SRR8201392/SRR8201392.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:52 18036313 reads; of these: 18036313 (100.00%) were unpaired; of these: 1748316 (9.69%) aligned 0 times 13638463 (75.62%) aligned exactly 1 time 2649534 (14.69%) aligned >1 times 90.31% overall alignment rate Time searching: 00:05:53 Overall time: 00:05:53 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] 3005367 / 16287997 = 0.1845 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 09:35:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020769/SRX5020769.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020769/SRX5020769.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020769/SRX5020769.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020769/SRX5020769.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 09:35:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:35:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:35:10: 1000000 INFO @ Tue, 16 Jun 2020 09:35:17: 2000000 INFO @ Tue, 16 Jun 2020 09:35:23: 3000000 INFO @ Tue, 16 Jun 2020 09:35:30: 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 09:35:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020769/SRX5020769.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020769/SRX5020769.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020769/SRX5020769.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020769/SRX5020769.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 09:35:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:35:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:35:37: 5000000 INFO @ Tue, 16 Jun 2020 09:35:42: 1000000 INFO @ Tue, 16 Jun 2020 09:35:45: 6000000 INFO @ Tue, 16 Jun 2020 09:35:50: 2000000 INFO @ Tue, 16 Jun 2020 09:35:53: 7000000 INFO @ Tue, 16 Jun 2020 09:35:58: 3000000 INFO @ Tue, 16 Jun 2020 09:36:01: 8000000 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 09:36:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020769/SRX5020769.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020769/SRX5020769.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020769/SRX5020769.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020769/SRX5020769.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 09:36:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:36:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:36:06: 4000000 INFO @ Tue, 16 Jun 2020 09:36:09: 9000000 INFO @ Tue, 16 Jun 2020 09:36:12: 1000000 INFO @ Tue, 16 Jun 2020 09:36:14: 5000000 INFO @ Tue, 16 Jun 2020 09:36:18: 10000000 INFO @ Tue, 16 Jun 2020 09:36:20: 2000000 INFO @ Tue, 16 Jun 2020 09:36:23: 6000000 INFO @ Tue, 16 Jun 2020 09:36:26: 11000000 INFO @ Tue, 16 Jun 2020 09:36:28: 3000000 INFO @ Tue, 16 Jun 2020 09:36:31: 7000000 INFO @ Tue, 16 Jun 2020 09:36:34: 12000000 INFO @ Tue, 16 Jun 2020 09:36:36: 4000000 INFO @ Tue, 16 Jun 2020 09:36:39: 8000000 INFO @ Tue, 16 Jun 2020 09:36:42: 13000000 INFO @ Tue, 16 Jun 2020 09:36:43: 5000000 INFO @ Tue, 16 Jun 2020 09:36:44: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:36:44: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:36:44: #1 total tags in treatment: 13282630 INFO @ Tue, 16 Jun 2020 09:36:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:44: #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 09:36:44: #1 tags after filtering in treatment: 13282630 INFO @ Tue, 16 Jun 2020 09:36:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:36:44: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:45: #2 number of paired peaks: 407 WARNING @ Tue, 16 Jun 2020 09:36:45: Fewer paired peaks (407) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 407 pairs to build model! INFO @ Tue, 16 Jun 2020 09:36:45: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:45: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:45: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:45: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:45: #2 predicted fragment length is 88 bps INFO @ Tue, 16 Jun 2020 09:36:45: #2 alternative fragment length(s) may be 4,88 bps INFO @ Tue, 16 Jun 2020 09:36:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020769/SRX5020769.05_model.r WARNING @ Tue, 16 Jun 2020 09:36:45: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:36:45: #2 You may need to consider one of the other alternative d(s): 4,88 WARNING @ Tue, 16 Jun 2020 09:36:45: #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 09:36:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:36:47: 9000000 INFO @ Tue, 16 Jun 2020 09:36:51: 6000000 INFO @ Tue, 16 Jun 2020 09:36:54: 10000000 INFO @ Tue, 16 Jun 2020 09:36:59: 7000000 INFO @ Tue, 16 Jun 2020 09:37:02: 11000000 INFO @ Tue, 16 Jun 2020 09:37:07: 8000000 INFO @ Tue, 16 Jun 2020 09:37:10: 12000000 INFO @ Tue, 16 Jun 2020 09:37:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:37:15: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:37:18: 13000000 INFO @ Tue, 16 Jun 2020 09:37:21: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:37:21: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:37:21: #1 total tags in treatment: 13282630 INFO @ Tue, 16 Jun 2020 09:37:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:37:21: #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 09:37:21: #1 tags after filtering in treatment: 13282630 INFO @ Tue, 16 Jun 2020 09:37:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:37:21: #1 finished! INFO @ Tue, 16 Jun 2020 09:37:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:37:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:37:22: #2 number of paired peaks: 407 WARNING @ Tue, 16 Jun 2020 09:37:22: Fewer paired peaks (407) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 407 pairs to build model! INFO @ Tue, 16 Jun 2020 09:37:22: start model_add_line... INFO @ Tue, 16 Jun 2020 09:37:22: start X-correlation... INFO @ Tue, 16 Jun 2020 09:37:22: end of X-cor INFO @ Tue, 16 Jun 2020 09:37:22: #2 finished! INFO @ Tue, 16 Jun 2020 09:37:22: #2 predicted fragment length is 88 bps INFO @ Tue, 16 Jun 2020 09:37:22: #2 alternative fragment length(s) may be 4,88 bps INFO @ Tue, 16 Jun 2020 09:37:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020769/SRX5020769.10_model.r WARNING @ Tue, 16 Jun 2020 09:37:22: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:37:22: #2 You may need to consider one of the other alternative d(s): 4,88 WARNING @ Tue, 16 Jun 2020 09:37:22: #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 09:37:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:37:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:37:23: 10000000 INFO @ Tue, 16 Jun 2020 09:37:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020769/SRX5020769.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:37:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020769/SRX5020769.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:37:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020769/SRX5020769.05_summits.bed INFO @ Tue, 16 Jun 2020 09:37:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1022 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:37:30: 11000000 INFO @ Tue, 16 Jun 2020 09:37:38: 12000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:37:45: 13000000 INFO @ Tue, 16 Jun 2020 09:37:47: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:37:47: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:37:47: #1 total tags in treatment: 13282630 INFO @ Tue, 16 Jun 2020 09:37:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:37:47: #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 09:37:47: #1 tags after filtering in treatment: 13282630 INFO @ Tue, 16 Jun 2020 09:37:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:37:47: #1 finished! INFO @ Tue, 16 Jun 2020 09:37:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:37:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:37:48: #2 number of paired peaks: 407 WARNING @ Tue, 16 Jun 2020 09:37:48: Fewer paired peaks (407) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 407 pairs to build model! INFO @ Tue, 16 Jun 2020 09:37:48: 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 88 bps INFO @ Tue, 16 Jun 2020 09:37:48: #2 alternative fragment length(s) may be 4,88 bps INFO @ Tue, 16 Jun 2020 09:37:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020769/SRX5020769.20_model.r WARNING @ Tue, 16 Jun 2020 09:37:48: #2 Since the d (88) 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): 4,88 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 09:37:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:38:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020769/SRX5020769.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:38:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020769/SRX5020769.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:38:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020769/SRX5020769.10_summits.bed INFO @ Tue, 16 Jun 2020 09:38:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (565 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:38:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:38:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020769/SRX5020769.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:38:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020769/SRX5020769.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:38:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020769/SRX5020769.20_summits.bed INFO @ Tue, 16 Jun 2020 09:38:25: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (309 records, 4 fields): 1 millis CompletedMACS2peakCalling