Job ID = 6497423 SRX = SRX494835 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:15:44 prefetch.2.10.7: 1) Downloading 'SRR1198367'... 2020-06-25T22:15:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:17:51 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:17:51 prefetch.2.10.7: 1) 'SRR1198367' was downloaded successfully Read 23497136 spots for SRR1198367/SRR1198367.sra Written 23497136 spots for SRR1198367/SRR1198367.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: 00:05:14 23497136 reads; of these: 23497136 (100.00%) were unpaired; of these: 270900 (1.15%) aligned 0 times 19081721 (81.21%) aligned exactly 1 time 4144515 (17.64%) aligned >1 times 98.85% overall alignment rate Time searching: 00:05:14 Overall time: 00:05:14 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] 9517862 / 23226236 = 0.4098 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 @ Fri, 26 Jun 2020 07:30:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494835/SRX494835.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494835/SRX494835.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494835/SRX494835.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494835/SRX494835.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 @ Fri, 26 Jun 2020 07:30:01: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:30:01: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:30:07: 1000000 INFO @ Fri, 26 Jun 2020 07:30:12: 2000000 INFO @ Fri, 26 Jun 2020 07:30:17: 3000000 INFO @ Fri, 26 Jun 2020 07:30:21: 4000000 INFO @ Fri, 26 Jun 2020 07:30:26: 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 @ Fri, 26 Jun 2020 07:30:31: 6000000 INFO @ Fri, 26 Jun 2020 07:30:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494835/SRX494835.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494835/SRX494835.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494835/SRX494835.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494835/SRX494835.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 @ Fri, 26 Jun 2020 07:30:31: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:30:31: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:30:37: 7000000 INFO @ Fri, 26 Jun 2020 07:30:37: 1000000 INFO @ Fri, 26 Jun 2020 07:30:42: 8000000 INFO @ Fri, 26 Jun 2020 07:30:42: 2000000 INFO @ Fri, 26 Jun 2020 07:30:48: 9000000 INFO @ Fri, 26 Jun 2020 07:30:48: 3000000 INFO @ Fri, 26 Jun 2020 07:30:53: 10000000 INFO @ Fri, 26 Jun 2020 07:30:54: 4000000 INFO @ Fri, 26 Jun 2020 07:30:59: 11000000 INFO @ Fri, 26 Jun 2020 07:31:00: 5000000 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 @ Fri, 26 Jun 2020 07:31:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494835/SRX494835.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494835/SRX494835.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494835/SRX494835.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494835/SRX494835.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 @ Fri, 26 Jun 2020 07:31:01: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:31:01: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:31:04: 12000000 INFO @ Fri, 26 Jun 2020 07:31:05: 6000000 INFO @ Fri, 26 Jun 2020 07:31:07: 1000000 INFO @ Fri, 26 Jun 2020 07:31:09: 13000000 INFO @ Fri, 26 Jun 2020 07:31:10: 7000000 INFO @ Fri, 26 Jun 2020 07:31:12: 2000000 INFO @ Fri, 26 Jun 2020 07:31:13: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:31:13: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:31:13: #1 total tags in treatment: 13708374 INFO @ Fri, 26 Jun 2020 07:31:13: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:31:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:31:13: #1 tags after filtering in treatment: 13708374 INFO @ Fri, 26 Jun 2020 07:31:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:31:13: #1 finished! INFO @ Fri, 26 Jun 2020 07:31:13: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:31:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:31:14: #2 number of paired peaks: 387 WARNING @ Fri, 26 Jun 2020 07:31:14: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Fri, 26 Jun 2020 07:31:14: start model_add_line... INFO @ Fri, 26 Jun 2020 07:31:14: start X-correlation... INFO @ Fri, 26 Jun 2020 07:31:14: end of X-cor INFO @ Fri, 26 Jun 2020 07:31:14: #2 finished! INFO @ Fri, 26 Jun 2020 07:31:14: #2 predicted fragment length is 43 bps INFO @ Fri, 26 Jun 2020 07:31:14: #2 alternative fragment length(s) may be 2,43 bps INFO @ Fri, 26 Jun 2020 07:31:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494835/SRX494835.05_model.r WARNING @ Fri, 26 Jun 2020 07:31:14: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:31:14: #2 You may need to consider one of the other alternative d(s): 2,43 WARNING @ Fri, 26 Jun 2020 07:31:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:31:14: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:31:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:31:16: 8000000 INFO @ Fri, 26 Jun 2020 07:31:18: 3000000 INFO @ Fri, 26 Jun 2020 07:31:21: 9000000 INFO @ Fri, 26 Jun 2020 07:31:23: 4000000 INFO @ Fri, 26 Jun 2020 07:31:26: 10000000 INFO @ Fri, 26 Jun 2020 07:31:28: 5000000 INFO @ Fri, 26 Jun 2020 07:31:32: 11000000 INFO @ Fri, 26 Jun 2020 07:31:33: 6000000 INFO @ Fri, 26 Jun 2020 07:31:37: 12000000 INFO @ Fri, 26 Jun 2020 07:31:39: 7000000 INFO @ Fri, 26 Jun 2020 07:31:40: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:31:42: 13000000 INFO @ Fri, 26 Jun 2020 07:31:44: 8000000 INFO @ Fri, 26 Jun 2020 07:31:46: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:31:46: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:31:46: #1 total tags in treatment: 13708374 INFO @ Fri, 26 Jun 2020 07:31:46: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:31:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:31:46: #1 tags after filtering in treatment: 13708374 INFO @ Fri, 26 Jun 2020 07:31:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:31:46: #1 finished! INFO @ Fri, 26 Jun 2020 07:31:46: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:31:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:31:47: #2 number of paired peaks: 387 WARNING @ Fri, 26 Jun 2020 07:31:47: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Fri, 26 Jun 2020 07:31:47: start model_add_line... INFO @ Fri, 26 Jun 2020 07:31:47: start X-correlation... INFO @ Fri, 26 Jun 2020 07:31:47: end of X-cor INFO @ Fri, 26 Jun 2020 07:31:47: #2 finished! INFO @ Fri, 26 Jun 2020 07:31:47: #2 predicted fragment length is 43 bps INFO @ Fri, 26 Jun 2020 07:31:47: #2 alternative fragment length(s) may be 2,43 bps INFO @ Fri, 26 Jun 2020 07:31:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494835/SRX494835.10_model.r WARNING @ Fri, 26 Jun 2020 07:31:47: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:31:47: #2 You may need to consider one of the other alternative d(s): 2,43 WARNING @ Fri, 26 Jun 2020 07:31:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:31:47: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:31:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:31:49: 9000000 INFO @ Fri, 26 Jun 2020 07:31:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494835/SRX494835.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:31:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494835/SRX494835.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:31:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494835/SRX494835.05_summits.bed INFO @ Fri, 26 Jun 2020 07:31:52: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (820 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:31:54: 10000000 INFO @ Fri, 26 Jun 2020 07:31:59: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:32:05: 12000000 INFO @ Fri, 26 Jun 2020 07:32:10: 13000000 INFO @ Fri, 26 Jun 2020 07:32:13: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:32:13: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:32:13: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:32:13: #1 total tags in treatment: 13708374 INFO @ Fri, 26 Jun 2020 07:32:13: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:32:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:32:14: #1 tags after filtering in treatment: 13708374 INFO @ Fri, 26 Jun 2020 07:32:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:32:14: #1 finished! INFO @ Fri, 26 Jun 2020 07:32:14: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:32:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:32:14: #2 number of paired peaks: 387 WARNING @ Fri, 26 Jun 2020 07:32:14: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Fri, 26 Jun 2020 07:32:14: start model_add_line... INFO @ Fri, 26 Jun 2020 07:32:15: start X-correlation... INFO @ Fri, 26 Jun 2020 07:32:15: end of X-cor INFO @ Fri, 26 Jun 2020 07:32:15: #2 finished! INFO @ Fri, 26 Jun 2020 07:32:15: #2 predicted fragment length is 43 bps INFO @ Fri, 26 Jun 2020 07:32:15: #2 alternative fragment length(s) may be 2,43 bps INFO @ Fri, 26 Jun 2020 07:32:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494835/SRX494835.20_model.r WARNING @ Fri, 26 Jun 2020 07:32:15: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:32:15: #2 You may need to consider one of the other alternative d(s): 2,43 WARNING @ Fri, 26 Jun 2020 07:32:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:32:15: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:32:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:32:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494835/SRX494835.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:32:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494835/SRX494835.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:32:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494835/SRX494835.10_summits.bed INFO @ Fri, 26 Jun 2020 07:32:25: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (540 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:32:40: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:32:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494835/SRX494835.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:32:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494835/SRX494835.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:32:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494835/SRX494835.20_summits.bed INFO @ Fri, 26 Jun 2020 07:32:52: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (207 records, 4 fields): 2 millis CompletedMACS2peakCalling