Job ID = 6367001 SRX = SRX257700 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 'SRR800717'... 2020-06-15T23:09:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:10:52 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:10:52 prefetch.2.10.7: 1) 'SRR800717' was downloaded successfully Read 18812743 spots for SRR800717/SRR800717.sra Written 18812743 spots for SRR800717/SRR800717.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: 00:04:24 18812743 reads; of these: 18812743 (100.00%) were unpaired; of these: 149797 (0.80%) aligned 0 times 15591129 (82.88%) aligned exactly 1 time 3071817 (16.33%) aligned >1 times 99.20% overall alignment rate Time searching: 00:04:24 Overall time: 00:04:24 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] 8433877 / 18662946 = 0.4519 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 08:20:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257700/SRX257700.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257700/SRX257700.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257700/SRX257700.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257700/SRX257700.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 08:20:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:20:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:20:26: 1000000 INFO @ Tue, 16 Jun 2020 08:20:32: 2000000 INFO @ Tue, 16 Jun 2020 08:20:38: 3000000 INFO @ Tue, 16 Jun 2020 08:20:44: 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 08:20:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257700/SRX257700.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257700/SRX257700.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257700/SRX257700.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257700/SRX257700.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 08:20:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:20:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:20:50: 5000000 INFO @ Tue, 16 Jun 2020 08:20:56: 1000000 INFO @ Tue, 16 Jun 2020 08:20:57: 6000000 INFO @ Tue, 16 Jun 2020 08:21:03: 2000000 INFO @ Tue, 16 Jun 2020 08:21:04: 7000000 INFO @ Tue, 16 Jun 2020 08:21:10: 3000000 INFO @ Tue, 16 Jun 2020 08:21:10: 8000000 INFO @ Tue, 16 Jun 2020 08:21:17: 4000000 INFO @ Tue, 16 Jun 2020 08:21:17: 9000000 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 08:21:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257700/SRX257700.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257700/SRX257700.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257700/SRX257700.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257700/SRX257700.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 08:21:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:21:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:21:24: 5000000 INFO @ Tue, 16 Jun 2020 08:21:24: 10000000 INFO @ Tue, 16 Jun 2020 08:21:25: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:21:25: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:21:25: #1 total tags in treatment: 10229069 INFO @ Tue, 16 Jun 2020 08:21:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:21:25: #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 08:21:26: #1 tags after filtering in treatment: 10229069 INFO @ Tue, 16 Jun 2020 08:21:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:21:26: #1 finished! INFO @ Tue, 16 Jun 2020 08:21:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:21:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:21:26: #2 number of paired peaks: 426 WARNING @ Tue, 16 Jun 2020 08:21:26: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Tue, 16 Jun 2020 08:21:26: start model_add_line... INFO @ Tue, 16 Jun 2020 08:21:26: start X-correlation... INFO @ Tue, 16 Jun 2020 08:21:26: end of X-cor INFO @ Tue, 16 Jun 2020 08:21:26: #2 finished! INFO @ Tue, 16 Jun 2020 08:21:26: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:21:26: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 16 Jun 2020 08:21:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257700/SRX257700.05_model.r WARNING @ Tue, 16 Jun 2020 08:21:26: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:21:26: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 16 Jun 2020 08:21:26: #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 08:21:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:21:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:21:27: 1000000 INFO @ Tue, 16 Jun 2020 08:21:30: 6000000 INFO @ Tue, 16 Jun 2020 08:21:34: 2000000 INFO @ Tue, 16 Jun 2020 08:21:37: 7000000 INFO @ Tue, 16 Jun 2020 08:21:40: 3000000 INFO @ Tue, 16 Jun 2020 08:21:44: 8000000 INFO @ Tue, 16 Jun 2020 08:21:47: 4000000 INFO @ Tue, 16 Jun 2020 08:21:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:51: 9000000 INFO @ Tue, 16 Jun 2020 08:21:54: 5000000 INFO @ Tue, 16 Jun 2020 08:21:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257700/SRX257700.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257700/SRX257700.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257700/SRX257700.05_summits.bed INFO @ Tue, 16 Jun 2020 08:21:58: Done! INFO @ Tue, 16 Jun 2020 08:21:58: 10000000 pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (761 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:21:59: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:21:59: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:21:59: #1 total tags in treatment: 10229069 INFO @ Tue, 16 Jun 2020 08:21:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:21:59: #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 08:22:00: #1 tags after filtering in treatment: 10229069 INFO @ Tue, 16 Jun 2020 08:22:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:22:00: #1 finished! INFO @ Tue, 16 Jun 2020 08:22:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:22:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:22:00: #2 number of paired peaks: 426 WARNING @ Tue, 16 Jun 2020 08:22:00: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Tue, 16 Jun 2020 08:22:00: start model_add_line... INFO @ Tue, 16 Jun 2020 08:22:00: start X-correlation... INFO @ Tue, 16 Jun 2020 08:22:00: end of X-cor INFO @ Tue, 16 Jun 2020 08:22:00: #2 finished! INFO @ Tue, 16 Jun 2020 08:22:00: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:22:00: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 16 Jun 2020 08:22:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257700/SRX257700.10_model.r WARNING @ Tue, 16 Jun 2020 08:22:00: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:22:00: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 16 Jun 2020 08:22:00: #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 08:22:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:22:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:22:01: 6000000 INFO @ Tue, 16 Jun 2020 08:22:07: 7000000 INFO @ Tue, 16 Jun 2020 08:22:14: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:22:21: 9000000 INFO @ Tue, 16 Jun 2020 08:22:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:22:28: 10000000 INFO @ Tue, 16 Jun 2020 08:22:30: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:22:30: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:22:30: #1 total tags in treatment: 10229069 INFO @ Tue, 16 Jun 2020 08:22:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:22:30: #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 08:22:30: #1 tags after filtering in treatment: 10229069 INFO @ Tue, 16 Jun 2020 08:22:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:22:30: #1 finished! INFO @ Tue, 16 Jun 2020 08:22:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:22:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:22:31: #2 number of paired peaks: 426 WARNING @ Tue, 16 Jun 2020 08:22:31: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Tue, 16 Jun 2020 08:22:31: start model_add_line... INFO @ Tue, 16 Jun 2020 08:22:31: start X-correlation... INFO @ Tue, 16 Jun 2020 08:22:31: end of X-cor INFO @ Tue, 16 Jun 2020 08:22:31: #2 finished! INFO @ Tue, 16 Jun 2020 08:22:31: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:22:31: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 16 Jun 2020 08:22:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257700/SRX257700.20_model.r WARNING @ Tue, 16 Jun 2020 08:22:31: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:22:31: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 16 Jun 2020 08:22:31: #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 08:22:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:22:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:22:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257700/SRX257700.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:22:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257700/SRX257700.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:22:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257700/SRX257700.10_summits.bed INFO @ Tue, 16 Jun 2020 08:22:32: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (553 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:22:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:23:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257700/SRX257700.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:23:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257700/SRX257700.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:23:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257700/SRX257700.20_summits.bed INFO @ Tue, 16 Jun 2020 08:23:03: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (219 records, 4 fields): 2 millis CompletedMACS2peakCalling