Job ID = 6367109 SRX = SRX277066 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:15:16 prefetch.2.10.7: 1) Downloading 'SRR849742'... 2020-06-15T23:15:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:15:46 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:15:46 prefetch.2.10.7: 'SRR849742' is valid 2020-06-15T23:15:46 prefetch.2.10.7: 1) 'SRR849742' was downloaded successfully Read 3781526 spots for SRR849742/SRR849742.sra Written 3781526 spots for SRR849742/SRR849742.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: 00:00:40 3781526 reads; of these: 3781526 (100.00%) were unpaired; of these: 93753 (2.48%) aligned 0 times 3055233 (80.79%) aligned exactly 1 time 632540 (16.73%) aligned >1 times 97.52% overall alignment rate Time searching: 00:00:40 Overall time: 00:00:40 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_rmdupse_core] 145784 / 3687773 = 0.0395 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 08:17:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277066/SRX277066.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277066/SRX277066.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277066/SRX277066.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277066/SRX277066.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 08:17:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:17:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:17:57: 1000000 INFO @ Tue, 16 Jun 2020 08:18:02: 2000000 INFO @ Tue, 16 Jun 2020 08:18:07: 3000000 INFO @ Tue, 16 Jun 2020 08:18:10: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:18:10: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:18:10: #1 total tags in treatment: 3541989 INFO @ Tue, 16 Jun 2020 08:18:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:18:10: #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 08:18:10: #1 tags after filtering in treatment: 3541989 INFO @ Tue, 16 Jun 2020 08:18:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:18:10: #1 finished! INFO @ Tue, 16 Jun 2020 08:18:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:18:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:18:10: #2 number of paired peaks: 431 WARNING @ Tue, 16 Jun 2020 08:18:10: Fewer paired peaks (431) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 431 pairs to build model! INFO @ Tue, 16 Jun 2020 08:18:10: start model_add_line... INFO @ Tue, 16 Jun 2020 08:18:10: start X-correlation... INFO @ Tue, 16 Jun 2020 08:18:10: end of X-cor INFO @ Tue, 16 Jun 2020 08:18:10: #2 finished! INFO @ Tue, 16 Jun 2020 08:18:10: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:18:10: #2 alternative fragment length(s) may be 4,31,522 bps INFO @ Tue, 16 Jun 2020 08:18:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277066/SRX277066.05_model.r WARNING @ Tue, 16 Jun 2020 08:18:10: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:18:10: #2 You may need to consider one of the other alternative d(s): 4,31,522 WARNING @ Tue, 16 Jun 2020 08:18:10: #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 08:18:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:18:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:18:17: #3 Call peaks for each chromosome... 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 08:18:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277066/SRX277066.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277066/SRX277066.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277066/SRX277066.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277066/SRX277066.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 08:18:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:18:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:18:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277066/SRX277066.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:18:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277066/SRX277066.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:18:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277066/SRX277066.05_summits.bed INFO @ Tue, 16 Jun 2020 08:18:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (375 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:18:25: 1000000 INFO @ Tue, 16 Jun 2020 08:18:29: 2000000 INFO @ Tue, 16 Jun 2020 08:18:33: 3000000 INFO @ Tue, 16 Jun 2020 08:18:36: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:18:36: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:18:36: #1 total tags in treatment: 3541989 INFO @ Tue, 16 Jun 2020 08:18:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:18:36: #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 08:18:36: #1 tags after filtering in treatment: 3541989 INFO @ Tue, 16 Jun 2020 08:18:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:18:36: #1 finished! INFO @ Tue, 16 Jun 2020 08:18:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:18:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:18:36: #2 number of paired peaks: 431 WARNING @ Tue, 16 Jun 2020 08:18:36: Fewer paired peaks (431) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 431 pairs to build model! INFO @ Tue, 16 Jun 2020 08:18:36: start model_add_line... INFO @ Tue, 16 Jun 2020 08:18:36: start X-correlation... INFO @ Tue, 16 Jun 2020 08:18:36: end of X-cor INFO @ Tue, 16 Jun 2020 08:18:36: #2 finished! INFO @ Tue, 16 Jun 2020 08:18:36: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:18:36: #2 alternative fragment length(s) may be 4,31,522 bps INFO @ Tue, 16 Jun 2020 08:18:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277066/SRX277066.10_model.r WARNING @ Tue, 16 Jun 2020 08:18:36: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:18:36: #2 You may need to consider one of the other alternative d(s): 4,31,522 WARNING @ Tue, 16 Jun 2020 08:18:36: #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 08:18:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:18:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:18:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:18:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277066/SRX277066.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:18:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277066/SRX277066.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:18:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277066/SRX277066.10_summits.bed INFO @ Tue, 16 Jun 2020 08:18:47: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (184 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 08:18:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277066/SRX277066.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277066/SRX277066.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277066/SRX277066.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277066/SRX277066.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 08:18:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:18:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:18:55: 1000000 INFO @ Tue, 16 Jun 2020 08:19:01: 2000000 INFO @ Tue, 16 Jun 2020 08:19:06: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:19:09: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:19:09: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:19:09: #1 total tags in treatment: 3541989 INFO @ Tue, 16 Jun 2020 08:19:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:19:09: #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 08:19:09: #1 tags after filtering in treatment: 3541989 INFO @ Tue, 16 Jun 2020 08:19:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:19:09: #1 finished! INFO @ Tue, 16 Jun 2020 08:19:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:19:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:19:09: #2 number of paired peaks: 431 WARNING @ Tue, 16 Jun 2020 08:19:09: Fewer paired peaks (431) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 431 pairs to build model! INFO @ Tue, 16 Jun 2020 08:19:09: start model_add_line... INFO @ Tue, 16 Jun 2020 08:19:09: start X-correlation... INFO @ Tue, 16 Jun 2020 08:19:09: end of X-cor INFO @ Tue, 16 Jun 2020 08:19:09: #2 finished! INFO @ Tue, 16 Jun 2020 08:19:09: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:19:09: #2 alternative fragment length(s) may be 4,31,522 bps INFO @ Tue, 16 Jun 2020 08:19:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277066/SRX277066.20_model.r WARNING @ Tue, 16 Jun 2020 08:19:09: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:19:09: #2 You may need to consider one of the other alternative d(s): 4,31,522 WARNING @ Tue, 16 Jun 2020 08:19:09: #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 08:19:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:19:09: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:19:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:19:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277066/SRX277066.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:19:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277066/SRX277066.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:19:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277066/SRX277066.20_summits.bed INFO @ Tue, 16 Jun 2020 08:19:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (58 records, 4 fields): 1 millis CompletedMACS2peakCalling