Job ID = 6367595 SRX = SRX331352 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:27:21 prefetch.2.10.7: 1) Downloading 'SRR947589'... 2020-06-15T23:27:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:31:43 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:31:43 prefetch.2.10.7: 1) 'SRR947589' was downloaded successfully Read 25432513 spots for SRR947589/SRR947589.sra Written 25432513 spots for SRR947589/SRR947589.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: 00:05:29 25432513 reads; of these: 25432513 (100.00%) were unpaired; of these: 1111612 (4.37%) aligned 0 times 20489256 (80.56%) aligned exactly 1 time 3831645 (15.07%) aligned >1 times 95.63% overall alignment rate Time searching: 00:05:29 Overall time: 00:05:29 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] 5818675 / 24320901 = 0.2392 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 08:44:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331352/SRX331352.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331352/SRX331352.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331352/SRX331352.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331352/SRX331352.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 08:44:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:44:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:44:30: 1000000 INFO @ Tue, 16 Jun 2020 08:44:36: 2000000 INFO @ Tue, 16 Jun 2020 08:44:42: 3000000 INFO @ Tue, 16 Jun 2020 08:44:48: 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 08:44:53: 5000000 INFO @ Tue, 16 Jun 2020 08:44:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331352/SRX331352.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331352/SRX331352.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331352/SRX331352.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331352/SRX331352.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 08:44:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:44:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:45:00: 6000000 INFO @ Tue, 16 Jun 2020 08:45:02: 1000000 INFO @ Tue, 16 Jun 2020 08:45:07: 7000000 INFO @ Tue, 16 Jun 2020 08:45:09: 2000000 INFO @ Tue, 16 Jun 2020 08:45:13: 8000000 INFO @ Tue, 16 Jun 2020 08:45:16: 3000000 INFO @ Tue, 16 Jun 2020 08:45:20: 9000000 INFO @ Tue, 16 Jun 2020 08:45:22: 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 08:45:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331352/SRX331352.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331352/SRX331352.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331352/SRX331352.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331352/SRX331352.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 08:45:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:45:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:45:27: 10000000 INFO @ Tue, 16 Jun 2020 08:45:29: 5000000 INFO @ Tue, 16 Jun 2020 08:45:32: 1000000 INFO @ Tue, 16 Jun 2020 08:45:33: 11000000 INFO @ Tue, 16 Jun 2020 08:45:36: 6000000 INFO @ Tue, 16 Jun 2020 08:45:39: 2000000 INFO @ Tue, 16 Jun 2020 08:45:40: 12000000 INFO @ Tue, 16 Jun 2020 08:45:43: 7000000 INFO @ Tue, 16 Jun 2020 08:45:46: 3000000 INFO @ Tue, 16 Jun 2020 08:45:47: 13000000 INFO @ Tue, 16 Jun 2020 08:45:50: 8000000 INFO @ Tue, 16 Jun 2020 08:45:52: 4000000 INFO @ Tue, 16 Jun 2020 08:45:54: 14000000 INFO @ Tue, 16 Jun 2020 08:45:57: 9000000 INFO @ Tue, 16 Jun 2020 08:45:59: 5000000 INFO @ Tue, 16 Jun 2020 08:46:01: 15000000 INFO @ Tue, 16 Jun 2020 08:46:04: 10000000 INFO @ Tue, 16 Jun 2020 08:46:06: 6000000 INFO @ Tue, 16 Jun 2020 08:46:07: 16000000 INFO @ Tue, 16 Jun 2020 08:46:11: 11000000 INFO @ Tue, 16 Jun 2020 08:46:13: 7000000 INFO @ Tue, 16 Jun 2020 08:46:14: 17000000 INFO @ Tue, 16 Jun 2020 08:46:17: 12000000 INFO @ Tue, 16 Jun 2020 08:46:19: 8000000 INFO @ Tue, 16 Jun 2020 08:46:21: 18000000 INFO @ Tue, 16 Jun 2020 08:46:24: 13000000 INFO @ Tue, 16 Jun 2020 08:46:24: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:46:24: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:46:24: #1 total tags in treatment: 18502226 INFO @ Tue, 16 Jun 2020 08:46:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:46:24: #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 08:46:24: #1 tags after filtering in treatment: 18502226 INFO @ Tue, 16 Jun 2020 08:46:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:46:24: #1 finished! INFO @ Tue, 16 Jun 2020 08:46:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:46:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:46:26: #2 number of paired peaks: 203 WARNING @ Tue, 16 Jun 2020 08:46:26: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Tue, 16 Jun 2020 08:46:26: start model_add_line... INFO @ Tue, 16 Jun 2020 08:46:26: start X-correlation... INFO @ Tue, 16 Jun 2020 08:46:26: end of X-cor INFO @ Tue, 16 Jun 2020 08:46:26: #2 finished! INFO @ Tue, 16 Jun 2020 08:46:26: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 08:46:26: #2 alternative fragment length(s) may be 1,46,578,588,595 bps INFO @ Tue, 16 Jun 2020 08:46:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331352/SRX331352.05_model.r WARNING @ Tue, 16 Jun 2020 08:46:26: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:46:26: #2 You may need to consider one of the other alternative d(s): 1,46,578,588,595 WARNING @ Tue, 16 Jun 2020 08:46:26: #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 08:46:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:46:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:46:26: 9000000 INFO @ Tue, 16 Jun 2020 08:46:31: 14000000 INFO @ Tue, 16 Jun 2020 08:46:33: 10000000 INFO @ Tue, 16 Jun 2020 08:46:37: 15000000 INFO @ Tue, 16 Jun 2020 08:46:39: 11000000 INFO @ Tue, 16 Jun 2020 08:46:44: 16000000 INFO @ Tue, 16 Jun 2020 08:46:46: 12000000 INFO @ Tue, 16 Jun 2020 08:46:51: 17000000 INFO @ Tue, 16 Jun 2020 08:46:53: 13000000 INFO @ Tue, 16 Jun 2020 08:46:57: 18000000 INFO @ Tue, 16 Jun 2020 08:46:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:46:59: 14000000 INFO @ Tue, 16 Jun 2020 08:47:01: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:47:01: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:47:01: #1 total tags in treatment: 18502226 INFO @ Tue, 16 Jun 2020 08:47:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:47:01: #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 08:47:01: #1 tags after filtering in treatment: 18502226 INFO @ Tue, 16 Jun 2020 08:47:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:47:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:47:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:47:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:47:02: #2 number of paired peaks: 203 WARNING @ Tue, 16 Jun 2020 08:47:02: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Tue, 16 Jun 2020 08:47:02: start model_add_line... INFO @ Tue, 16 Jun 2020 08:47:02: start X-correlation... INFO @ Tue, 16 Jun 2020 08:47:02: end of X-cor INFO @ Tue, 16 Jun 2020 08:47:02: #2 finished! INFO @ Tue, 16 Jun 2020 08:47:02: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 08:47:02: #2 alternative fragment length(s) may be 1,46,578,588,595 bps INFO @ Tue, 16 Jun 2020 08:47:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331352/SRX331352.10_model.r WARNING @ Tue, 16 Jun 2020 08:47:02: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:47:02: #2 You may need to consider one of the other alternative d(s): 1,46,578,588,595 WARNING @ Tue, 16 Jun 2020 08:47:02: #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 08:47:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:47:02: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:47:06: 15000000 INFO @ Tue, 16 Jun 2020 08:47:12: 16000000 INFO @ Tue, 16 Jun 2020 08:47:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331352/SRX331352.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:47:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331352/SRX331352.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:47:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331352/SRX331352.05_summits.bed INFO @ Tue, 16 Jun 2020 08:47:13: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (721 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:47:18: 17000000 INFO @ Tue, 16 Jun 2020 08:47:23: 18000000 INFO @ Tue, 16 Jun 2020 08:47:26: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:47:26: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:47:26: #1 total tags in treatment: 18502226 INFO @ Tue, 16 Jun 2020 08:47:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:47:26: #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 08:47:26: #1 tags after filtering in treatment: 18502226 INFO @ Tue, 16 Jun 2020 08:47:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:47:26: #1 finished! INFO @ Tue, 16 Jun 2020 08:47:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:47:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:47:27: #2 number of paired peaks: 203 WARNING @ Tue, 16 Jun 2020 08:47:27: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Tue, 16 Jun 2020 08:47:27: start model_add_line... INFO @ Tue, 16 Jun 2020 08:47:28: start X-correlation... INFO @ Tue, 16 Jun 2020 08:47:28: end of X-cor INFO @ Tue, 16 Jun 2020 08:47:28: #2 finished! INFO @ Tue, 16 Jun 2020 08:47:28: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 08:47:28: #2 alternative fragment length(s) may be 1,46,578,588,595 bps INFO @ Tue, 16 Jun 2020 08:47:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331352/SRX331352.20_model.r WARNING @ Tue, 16 Jun 2020 08:47:28: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:47:28: #2 You may need to consider one of the other alternative d(s): 1,46,578,588,595 WARNING @ Tue, 16 Jun 2020 08:47:28: #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 08:47:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:47:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:47:33: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:47:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331352/SRX331352.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:47:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331352/SRX331352.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:47:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331352/SRX331352.10_summits.bed INFO @ Tue, 16 Jun 2020 08:47:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (430 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:47:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:48:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331352/SRX331352.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:48:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331352/SRX331352.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:48:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331352/SRX331352.20_summits.bed INFO @ Tue, 16 Jun 2020 08:48:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (167 records, 4 fields): 1 millis CompletedMACS2peakCalling