Job ID = 6367045 SRX = SRX2761390 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:09:16 prefetch.2.10.7: 1) Downloading 'SRR5476964'... 2020-06-15T23:09:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:12:24 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:12:24 prefetch.2.10.7: 1) 'SRR5476964' was downloaded successfully Read 16597750 spots for SRR5476964/SRR5476964.sra Written 16597750 spots for SRR5476964/SRR5476964.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: 00:03:41 16597750 reads; of these: 16597750 (100.00%) were unpaired; of these: 720461 (4.34%) aligned 0 times 12952492 (78.04%) aligned exactly 1 time 2924797 (17.62%) aligned >1 times 95.66% overall alignment rate Time searching: 00:03:41 Overall time: 00:03:41 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] 1350928 / 15877289 = 0.0851 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 08:21:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2761390/SRX2761390.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2761390/SRX2761390.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2761390/SRX2761390.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2761390/SRX2761390.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 08:21:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:21:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:21:11: 1000000 INFO @ Tue, 16 Jun 2020 08:21:18: 2000000 INFO @ Tue, 16 Jun 2020 08:21:24: 3000000 INFO @ Tue, 16 Jun 2020 08:21:31: 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 08:21:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2761390/SRX2761390.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2761390/SRX2761390.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2761390/SRX2761390.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2761390/SRX2761390.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 08:21:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:21:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:21:38: 5000000 INFO @ Tue, 16 Jun 2020 08:21:42: 1000000 INFO @ Tue, 16 Jun 2020 08:21:45: 6000000 INFO @ Tue, 16 Jun 2020 08:21:48: 2000000 INFO @ Tue, 16 Jun 2020 08:21:51: 7000000 INFO @ Tue, 16 Jun 2020 08:21:55: 3000000 INFO @ Tue, 16 Jun 2020 08:21:58: 8000000 INFO @ Tue, 16 Jun 2020 08:22:02: 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 08:22:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2761390/SRX2761390.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2761390/SRX2761390.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2761390/SRX2761390.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2761390/SRX2761390.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 08:22:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:22:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:22:05: 9000000 INFO @ Tue, 16 Jun 2020 08:22:09: 5000000 INFO @ Tue, 16 Jun 2020 08:22:12: 1000000 INFO @ Tue, 16 Jun 2020 08:22:13: 10000000 INFO @ Tue, 16 Jun 2020 08:22:17: 6000000 INFO @ Tue, 16 Jun 2020 08:22:19: 2000000 INFO @ Tue, 16 Jun 2020 08:22:20: 11000000 INFO @ Tue, 16 Jun 2020 08:22:24: 7000000 INFO @ Tue, 16 Jun 2020 08:22:26: 3000000 INFO @ Tue, 16 Jun 2020 08:22:27: 12000000 INFO @ Tue, 16 Jun 2020 08:22:31: 8000000 INFO @ Tue, 16 Jun 2020 08:22:34: 4000000 INFO @ Tue, 16 Jun 2020 08:22:34: 13000000 INFO @ Tue, 16 Jun 2020 08:22:38: 9000000 INFO @ Tue, 16 Jun 2020 08:22:41: 5000000 INFO @ Tue, 16 Jun 2020 08:22:41: 14000000 INFO @ Tue, 16 Jun 2020 08:22:45: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:22:45: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:22:45: #1 total tags in treatment: 14526361 INFO @ Tue, 16 Jun 2020 08:22:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:22:45: #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 08:22:45: #1 tags after filtering in treatment: 14526361 INFO @ Tue, 16 Jun 2020 08:22:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:22:45: #1 finished! INFO @ Tue, 16 Jun 2020 08:22:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:22:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:22:45: 10000000 INFO @ Tue, 16 Jun 2020 08:22:46: #2 number of paired peaks: 372 WARNING @ Tue, 16 Jun 2020 08:22:46: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Tue, 16 Jun 2020 08:22:46: start model_add_line... INFO @ Tue, 16 Jun 2020 08:22:46: start X-correlation... INFO @ Tue, 16 Jun 2020 08:22:46: end of X-cor INFO @ Tue, 16 Jun 2020 08:22:46: #2 finished! INFO @ Tue, 16 Jun 2020 08:22:46: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 08:22:46: #2 alternative fragment length(s) may be 2,44 bps INFO @ Tue, 16 Jun 2020 08:22:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2761390/SRX2761390.05_model.r WARNING @ Tue, 16 Jun 2020 08:22:46: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:22:46: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Tue, 16 Jun 2020 08:22:46: #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 08:22:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:22:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:22:48: 6000000 INFO @ Tue, 16 Jun 2020 08:22:52: 11000000 INFO @ Tue, 16 Jun 2020 08:22:56: 7000000 INFO @ Tue, 16 Jun 2020 08:23:00: 12000000 INFO @ Tue, 16 Jun 2020 08:23:03: 8000000 INFO @ Tue, 16 Jun 2020 08:23:07: 13000000 INFO @ Tue, 16 Jun 2020 08:23:10: 9000000 INFO @ Tue, 16 Jun 2020 08:23:13: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:23:14: 14000000 INFO @ Tue, 16 Jun 2020 08:23:17: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:23:17: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:23:17: #1 total tags in treatment: 14526361 INFO @ Tue, 16 Jun 2020 08:23:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:23:17: #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 08:23:18: 10000000 INFO @ Tue, 16 Jun 2020 08:23:18: #1 tags after filtering in treatment: 14526361 INFO @ Tue, 16 Jun 2020 08:23:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:23:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:23:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:23:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:23:19: #2 number of paired peaks: 372 WARNING @ Tue, 16 Jun 2020 08:23:19: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Tue, 16 Jun 2020 08:23:19: start model_add_line... INFO @ Tue, 16 Jun 2020 08:23:19: start X-correlation... INFO @ Tue, 16 Jun 2020 08:23:19: end of X-cor INFO @ Tue, 16 Jun 2020 08:23:19: #2 finished! INFO @ Tue, 16 Jun 2020 08:23:19: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 08:23:19: #2 alternative fragment length(s) may be 2,44 bps INFO @ Tue, 16 Jun 2020 08:23:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2761390/SRX2761390.10_model.r WARNING @ Tue, 16 Jun 2020 08:23:19: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:23:19: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Tue, 16 Jun 2020 08:23:19: #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 08:23:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:23:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:23:24: 11000000 INFO @ Tue, 16 Jun 2020 08:23:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2761390/SRX2761390.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:23:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2761390/SRX2761390.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:23:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2761390/SRX2761390.05_summits.bed INFO @ Tue, 16 Jun 2020 08:23:26: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (754 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:23:31: 12000000 INFO @ Tue, 16 Jun 2020 08:23:37: 13000000 INFO @ Tue, 16 Jun 2020 08:23:44: 14000000 INFO @ Tue, 16 Jun 2020 08:23:45: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:23:47: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:23:47: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:23:47: #1 total tags in treatment: 14526361 INFO @ Tue, 16 Jun 2020 08:23:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:23:47: #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 08:23:47: #1 tags after filtering in treatment: 14526361 INFO @ Tue, 16 Jun 2020 08:23:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:23:47: #1 finished! INFO @ Tue, 16 Jun 2020 08:23:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:23:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:23:48: #2 number of paired peaks: 372 WARNING @ Tue, 16 Jun 2020 08:23:48: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Tue, 16 Jun 2020 08:23:48: start model_add_line... INFO @ Tue, 16 Jun 2020 08:23:49: start X-correlation... INFO @ Tue, 16 Jun 2020 08:23:49: end of X-cor INFO @ Tue, 16 Jun 2020 08:23:49: #2 finished! INFO @ Tue, 16 Jun 2020 08:23:49: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 08:23:49: #2 alternative fragment length(s) may be 2,44 bps INFO @ Tue, 16 Jun 2020 08:23:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2761390/SRX2761390.20_model.r WARNING @ Tue, 16 Jun 2020 08:23:49: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:23:49: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Tue, 16 Jun 2020 08:23:49: #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 08:23:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:23:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:23:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2761390/SRX2761390.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:23:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2761390/SRX2761390.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:23:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2761390/SRX2761390.10_summits.bed INFO @ Tue, 16 Jun 2020 08:23:57: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (511 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:24:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:24:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2761390/SRX2761390.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:24:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2761390/SRX2761390.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:24:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2761390/SRX2761390.20_summits.bed INFO @ Tue, 16 Jun 2020 08:24:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (196 records, 4 fields): 1 millis CompletedMACS2peakCalling