Job ID = 6368518 SRX = SRX5020747 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:12:50 prefetch.2.10.7: 1) Downloading 'SRR8201370'... 2020-06-16T00:12:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:14:43 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:14:44 prefetch.2.10.7: 'SRR8201370' is valid 2020-06-16T00:14:44 prefetch.2.10.7: 1) 'SRR8201370' was downloaded successfully 2020-06-16T00:14:44 prefetch.2.10.7: 'SRR8201370' has 0 unresolved dependencies Read 18065351 spots for SRR8201370/SRR8201370.sra Written 18065351 spots for SRR8201370/SRR8201370.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: 00:06:32 18065351 reads; of these: 18065351 (100.00%) were unpaired; of these: 275666 (1.53%) aligned 0 times 13630450 (75.45%) aligned exactly 1 time 4159235 (23.02%) aligned >1 times 98.47% overall alignment rate Time searching: 00:06:32 Overall time: 00:06:32 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] 2705589 / 17789685 = 0.1521 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 09:27:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020747/SRX5020747.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020747/SRX5020747.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020747/SRX5020747.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020747/SRX5020747.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 09:27:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:37: 1000000 INFO @ Tue, 16 Jun 2020 09:27:42: 2000000 INFO @ Tue, 16 Jun 2020 09:27:47: 3000000 INFO @ Tue, 16 Jun 2020 09:27:53: 4000000 INFO @ Tue, 16 Jun 2020 09:27:58: 5000000 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 09:28:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020747/SRX5020747.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020747/SRX5020747.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020747/SRX5020747.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020747/SRX5020747.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 09:28:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:04: 6000000 INFO @ Tue, 16 Jun 2020 09:28:08: 1000000 INFO @ Tue, 16 Jun 2020 09:28:09: 7000000 INFO @ Tue, 16 Jun 2020 09:28:14: 2000000 INFO @ Tue, 16 Jun 2020 09:28:15: 8000000 INFO @ Tue, 16 Jun 2020 09:28:20: 3000000 INFO @ Tue, 16 Jun 2020 09:28:20: 9000000 INFO @ Tue, 16 Jun 2020 09:28:26: 10000000 INFO @ Tue, 16 Jun 2020 09:28:26: 4000000 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 09:28:31: 11000000 INFO @ Tue, 16 Jun 2020 09:28:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020747/SRX5020747.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020747/SRX5020747.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020747/SRX5020747.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020747/SRX5020747.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 09:28:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:32: 5000000 INFO @ Tue, 16 Jun 2020 09:28:37: 12000000 INFO @ Tue, 16 Jun 2020 09:28:37: 1000000 INFO @ Tue, 16 Jun 2020 09:28:38: 6000000 INFO @ Tue, 16 Jun 2020 09:28:42: 13000000 INFO @ Tue, 16 Jun 2020 09:28:43: 2000000 INFO @ Tue, 16 Jun 2020 09:28:45: 7000000 INFO @ Tue, 16 Jun 2020 09:28:48: 14000000 INFO @ Tue, 16 Jun 2020 09:28:48: 3000000 INFO @ Tue, 16 Jun 2020 09:28:51: 8000000 INFO @ Tue, 16 Jun 2020 09:28:54: 15000000 INFO @ Tue, 16 Jun 2020 09:28:54: 4000000 INFO @ Tue, 16 Jun 2020 09:28:54: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:28:54: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:28:54: #1 total tags in treatment: 15084096 INFO @ Tue, 16 Jun 2020 09:28:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:28:54: #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 09:28:55: #1 tags after filtering in treatment: 15084096 INFO @ Tue, 16 Jun 2020 09:28:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:28:55: #1 finished! INFO @ Tue, 16 Jun 2020 09:28:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:28:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:28:56: #2 number of paired peaks: 706 WARNING @ Tue, 16 Jun 2020 09:28:56: Fewer paired peaks (706) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 706 pairs to build model! INFO @ Tue, 16 Jun 2020 09:28:56: start model_add_line... INFO @ Tue, 16 Jun 2020 09:28:56: start X-correlation... INFO @ Tue, 16 Jun 2020 09:28:56: end of X-cor INFO @ Tue, 16 Jun 2020 09:28:56: #2 finished! INFO @ Tue, 16 Jun 2020 09:28:56: #2 predicted fragment length is 74 bps INFO @ Tue, 16 Jun 2020 09:28:56: #2 alternative fragment length(s) may be 2,74,591 bps INFO @ Tue, 16 Jun 2020 09:28:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020747/SRX5020747.05_model.r WARNING @ Tue, 16 Jun 2020 09:28:56: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:28:56: #2 You may need to consider one of the other alternative d(s): 2,74,591 WARNING @ Tue, 16 Jun 2020 09:28:56: #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 09:28:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:28:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:28:57: 9000000 INFO @ Tue, 16 Jun 2020 09:28:59: 5000000 INFO @ Tue, 16 Jun 2020 09:29:03: 10000000 INFO @ Tue, 16 Jun 2020 09:29:05: 6000000 INFO @ Tue, 16 Jun 2020 09:29:09: 11000000 INFO @ Tue, 16 Jun 2020 09:29:11: 7000000 INFO @ Tue, 16 Jun 2020 09:29:15: 12000000 INFO @ Tue, 16 Jun 2020 09:29:16: 8000000 INFO @ Tue, 16 Jun 2020 09:29:21: 13000000 INFO @ Tue, 16 Jun 2020 09:29:22: 9000000 INFO @ Tue, 16 Jun 2020 09:29:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:29:27: 14000000 INFO @ Tue, 16 Jun 2020 09:29:27: 10000000 INFO @ Tue, 16 Jun 2020 09:29:33: 11000000 INFO @ Tue, 16 Jun 2020 09:29:33: 15000000 INFO @ Tue, 16 Jun 2020 09:29:34: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:29:34: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:29:34: #1 total tags in treatment: 15084096 INFO @ Tue, 16 Jun 2020 09:29:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:34: #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 09:29:34: #1 tags after filtering in treatment: 15084096 INFO @ Tue, 16 Jun 2020 09:29:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:29:34: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:29:35: #2 number of paired peaks: 706 WARNING @ Tue, 16 Jun 2020 09:29:35: Fewer paired peaks (706) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 706 pairs to build model! INFO @ Tue, 16 Jun 2020 09:29:35: start model_add_line... INFO @ Tue, 16 Jun 2020 09:29:35: start X-correlation... INFO @ Tue, 16 Jun 2020 09:29:35: end of X-cor INFO @ Tue, 16 Jun 2020 09:29:35: #2 finished! INFO @ Tue, 16 Jun 2020 09:29:35: #2 predicted fragment length is 74 bps INFO @ Tue, 16 Jun 2020 09:29:35: #2 alternative fragment length(s) may be 2,74,591 bps INFO @ Tue, 16 Jun 2020 09:29:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020747/SRX5020747.10_model.r WARNING @ Tue, 16 Jun 2020 09:29:35: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:29:35: #2 You may need to consider one of the other alternative d(s): 2,74,591 WARNING @ Tue, 16 Jun 2020 09:29:35: #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 09:29:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:29:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:29:38: 12000000 INFO @ Tue, 16 Jun 2020 09:29:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020747/SRX5020747.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:29:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020747/SRX5020747.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:29:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020747/SRX5020747.05_summits.bed INFO @ Tue, 16 Jun 2020 09:29:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1717 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:29:43: 13000000 INFO @ Tue, 16 Jun 2020 09:29:48: 14000000 INFO @ Tue, 16 Jun 2020 09:29:54: 15000000 INFO @ Tue, 16 Jun 2020 09:29:54: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:29:54: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:29:54: #1 total tags in treatment: 15084096 INFO @ Tue, 16 Jun 2020 09:29:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:54: #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 09:29:54: #1 tags after filtering in treatment: 15084096 INFO @ Tue, 16 Jun 2020 09:29:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:29:54: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:54: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:29:55: #2 number of paired peaks: 706 WARNING @ Tue, 16 Jun 2020 09:29:55: Fewer paired peaks (706) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 706 pairs to build model! INFO @ Tue, 16 Jun 2020 09:29:55: start model_add_line... INFO @ Tue, 16 Jun 2020 09:29:56: start X-correlation... INFO @ Tue, 16 Jun 2020 09:29:56: end of X-cor INFO @ Tue, 16 Jun 2020 09:29:56: #2 finished! INFO @ Tue, 16 Jun 2020 09:29:56: #2 predicted fragment length is 74 bps INFO @ Tue, 16 Jun 2020 09:29:56: #2 alternative fragment length(s) may be 2,74,591 bps INFO @ Tue, 16 Jun 2020 09:29:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020747/SRX5020747.20_model.r WARNING @ Tue, 16 Jun 2020 09:29:56: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:29:56: #2 You may need to consider one of the other alternative d(s): 2,74,591 WARNING @ Tue, 16 Jun 2020 09:29:56: #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 09:29:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:29:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:30:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:30:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020747/SRX5020747.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:30:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020747/SRX5020747.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:30:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020747/SRX5020747.10_summits.bed INFO @ Tue, 16 Jun 2020 09:30:19: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (643 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:30:25: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:30:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020747/SRX5020747.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:30:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020747/SRX5020747.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:30:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020747/SRX5020747.20_summits.bed INFO @ Tue, 16 Jun 2020 09:30:39: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (238 records, 4 fields): 2 millis CompletedMACS2peakCalling