Job ID = 6367080 SRX = SRX277038 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:12:16 prefetch.2.10.7: 1) Downloading 'SRR849706'... 2020-06-15T23:12:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:12:46 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:12:47 prefetch.2.10.7: 'SRR849706' is valid 2020-06-15T23:12:47 prefetch.2.10.7: 1) 'SRR849706' was downloaded successfully Read 4796181 spots for SRR849706/SRR849706.sra Written 4796181 spots for SRR849706/SRR849706.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: 00:00:53 4796181 reads; of these: 4796181 (100.00%) were unpaired; of these: 46134 (0.96%) aligned 0 times 3905248 (81.42%) aligned exactly 1 time 844799 (17.61%) aligned >1 times 99.04% overall alignment rate Time searching: 00:00:53 Overall time: 00:00:53 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] 434293 / 4750047 = 0.0914 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 08:15:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277038/SRX277038.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277038/SRX277038.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277038/SRX277038.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277038/SRX277038.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 08:15:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:25: 1000000 INFO @ Tue, 16 Jun 2020 08:15:31: 2000000 INFO @ Tue, 16 Jun 2020 08:15:36: 3000000 INFO @ Tue, 16 Jun 2020 08:15:42: 4000000 INFO @ Tue, 16 Jun 2020 08:15:44: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:15:44: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:15:44: #1 total tags in treatment: 4315754 INFO @ Tue, 16 Jun 2020 08:15:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:44: #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 08:15:44: #1 tags after filtering in treatment: 4315754 INFO @ Tue, 16 Jun 2020 08:15:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:44: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:44: #2 number of paired peaks: 396 WARNING @ Tue, 16 Jun 2020 08:15:44: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Tue, 16 Jun 2020 08:15:44: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:44: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:44: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:44: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:44: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:15:44: #2 alternative fragment length(s) may be 3,31,549,576 bps INFO @ Tue, 16 Jun 2020 08:15:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277038/SRX277038.05_model.r WARNING @ Tue, 16 Jun 2020 08:15:44: #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 08:15:44: #2 You may need to consider one of the other alternative d(s): 3,31,549,576 WARNING @ Tue, 16 Jun 2020 08:15:44: #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 08:15:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:44: #3 Pre-compute pvalue-qvalue table... 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 08:15:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277038/SRX277038.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277038/SRX277038.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277038/SRX277038.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277038/SRX277038.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 08:15:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:15:54: 1000000 INFO @ Tue, 16 Jun 2020 08:15:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277038/SRX277038.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277038/SRX277038.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277038/SRX277038.05_summits.bed INFO @ Tue, 16 Jun 2020 08:15:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (328 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:16:00: 2000000 INFO @ Tue, 16 Jun 2020 08:16:05: 3000000 INFO @ Tue, 16 Jun 2020 08:16:10: 4000000 INFO @ Tue, 16 Jun 2020 08:16:11: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:16:11: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:16:11: #1 total tags in treatment: 4315754 INFO @ Tue, 16 Jun 2020 08:16:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:16:11: #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 08:16:11: #1 tags after filtering in treatment: 4315754 INFO @ Tue, 16 Jun 2020 08:16:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:16:11: #1 finished! INFO @ Tue, 16 Jun 2020 08:16:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:16:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:16:12: #2 number of paired peaks: 396 WARNING @ Tue, 16 Jun 2020 08:16:12: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Tue, 16 Jun 2020 08:16:12: start model_add_line... INFO @ Tue, 16 Jun 2020 08:16:12: start X-correlation... INFO @ Tue, 16 Jun 2020 08:16:12: end of X-cor INFO @ Tue, 16 Jun 2020 08:16:12: #2 finished! INFO @ Tue, 16 Jun 2020 08:16:12: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:16:12: #2 alternative fragment length(s) may be 3,31,549,576 bps INFO @ Tue, 16 Jun 2020 08:16:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277038/SRX277038.10_model.r WARNING @ Tue, 16 Jun 2020 08:16:12: #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 08:16:12: #2 You may need to consider one of the other alternative d(s): 3,31,549,576 WARNING @ Tue, 16 Jun 2020 08:16:12: #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 08:16:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:16:12: #3 Pre-compute pvalue-qvalue table... 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 08:16:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277038/SRX277038.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277038/SRX277038.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277038/SRX277038.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277038/SRX277038.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 08:16:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:16:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:16:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:16:24: 1000000 INFO @ Tue, 16 Jun 2020 08:16:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277038/SRX277038.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:16:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277038/SRX277038.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:16:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277038/SRX277038.10_summits.bed INFO @ Tue, 16 Jun 2020 08:16:25: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (114 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:16:30: 2000000 INFO @ Tue, 16 Jun 2020 08:16:35: 3000000 INFO @ Tue, 16 Jun 2020 08:16:40: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:16:41: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:16:41: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:16:41: #1 total tags in treatment: 4315754 INFO @ Tue, 16 Jun 2020 08:16:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:16:41: #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 08:16:41: #1 tags after filtering in treatment: 4315754 INFO @ Tue, 16 Jun 2020 08:16:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:16:41: #1 finished! INFO @ Tue, 16 Jun 2020 08:16:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:16:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:16:42: #2 number of paired peaks: 396 WARNING @ Tue, 16 Jun 2020 08:16:42: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Tue, 16 Jun 2020 08:16:42: start model_add_line... INFO @ Tue, 16 Jun 2020 08:16:42: start X-correlation... INFO @ Tue, 16 Jun 2020 08:16:42: end of X-cor INFO @ Tue, 16 Jun 2020 08:16:42: #2 finished! INFO @ Tue, 16 Jun 2020 08:16:42: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:16:42: #2 alternative fragment length(s) may be 3,31,549,576 bps INFO @ Tue, 16 Jun 2020 08:16:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277038/SRX277038.20_model.r WARNING @ Tue, 16 Jun 2020 08:16:42: #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 08:16:42: #2 You may need to consider one of the other alternative d(s): 3,31,549,576 WARNING @ Tue, 16 Jun 2020 08:16:42: #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 08:16:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:16:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:16:51: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:16:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277038/SRX277038.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:16:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277038/SRX277038.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:16:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277038/SRX277038.20_summits.bed INFO @ Tue, 16 Jun 2020 08:16:55: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (11 records, 4 fields): 1 millis CompletedMACS2peakCalling