Job ID = 6367549 SRX = SRX331305 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:29:35 prefetch.2.10.7: 1) Downloading 'SRR947542'... 2020-06-15T23:29:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:29:57 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:29:57 prefetch.2.10.7: 'SRR947542' is valid 2020-06-15T23:29:57 prefetch.2.10.7: 1) 'SRR947542' was downloaded successfully Read 4434177 spots for SRR947542/SRR947542.sra Written 4434177 spots for SRR947542/SRR947542.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: 00:00:42 4434177 reads; of these: 4434177 (100.00%) were unpaired; of these: 27438 (0.62%) aligned 0 times 3692134 (83.27%) aligned exactly 1 time 714605 (16.12%) aligned >1 times 99.38% overall alignment rate Time searching: 00:00:42 Overall time: 00:00:42 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] 249226 / 4406739 = 0.0566 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 08:32:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331305/SRX331305.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331305/SRX331305.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331305/SRX331305.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331305/SRX331305.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 08:32:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:32:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:32:17: 1000000 INFO @ Tue, 16 Jun 2020 08:32:23: 2000000 INFO @ Tue, 16 Jun 2020 08:32:28: 3000000 INFO @ Tue, 16 Jun 2020 08:32:33: 4000000 INFO @ Tue, 16 Jun 2020 08:32:33: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:32:33: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:32:33: #1 total tags in treatment: 4157513 INFO @ Tue, 16 Jun 2020 08:32:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:33: #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 08:32:33: #1 tags after filtering in treatment: 4157513 INFO @ Tue, 16 Jun 2020 08:32:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:33: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:34: #2 number of paired peaks: 381 WARNING @ Tue, 16 Jun 2020 08:32:34: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Tue, 16 Jun 2020 08:32:34: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:34: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:34: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:34: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:34: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 08:32:34: #2 alternative fragment length(s) may be 4,38,411 bps INFO @ Tue, 16 Jun 2020 08:32:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331305/SRX331305.05_model.r WARNING @ Tue, 16 Jun 2020 08:32:34: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:32:34: #2 You may need to consider one of the other alternative d(s): 4,38,411 WARNING @ Tue, 16 Jun 2020 08:32:34: #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 08:32:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:34: #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 08:32:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331305/SRX331305.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331305/SRX331305.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331305/SRX331305.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331305/SRX331305.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 08:32:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:32:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:32:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:32:47: 1000000 INFO @ Tue, 16 Jun 2020 08:32:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331305/SRX331305.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:32:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331305/SRX331305.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:32:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331305/SRX331305.05_summits.bed INFO @ Tue, 16 Jun 2020 08:32:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (387 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:32:53: 2000000 INFO @ Tue, 16 Jun 2020 08:32:58: 3000000 INFO @ Tue, 16 Jun 2020 08:33:03: 4000000 INFO @ Tue, 16 Jun 2020 08:33:03: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:33:03: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:33:03: #1 total tags in treatment: 4157513 INFO @ Tue, 16 Jun 2020 08:33:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:33:03: #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 08:33:03: #1 tags after filtering in treatment: 4157513 INFO @ Tue, 16 Jun 2020 08:33:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:33:03: #1 finished! INFO @ Tue, 16 Jun 2020 08:33:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:33:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:33:04: #2 number of paired peaks: 381 WARNING @ Tue, 16 Jun 2020 08:33:04: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Tue, 16 Jun 2020 08:33:04: start model_add_line... INFO @ Tue, 16 Jun 2020 08:33:04: start X-correlation... INFO @ Tue, 16 Jun 2020 08:33:04: end of X-cor INFO @ Tue, 16 Jun 2020 08:33:04: #2 finished! INFO @ Tue, 16 Jun 2020 08:33:04: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 08:33:04: #2 alternative fragment length(s) may be 4,38,411 bps INFO @ Tue, 16 Jun 2020 08:33:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331305/SRX331305.10_model.r WARNING @ Tue, 16 Jun 2020 08:33:04: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:33:04: #2 You may need to consider one of the other alternative d(s): 4,38,411 WARNING @ Tue, 16 Jun 2020 08:33:04: #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 08:33:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:33:04: #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 08:33:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:33:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331305/SRX331305.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331305/SRX331305.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331305/SRX331305.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331305/SRX331305.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 08:33:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:33:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:33:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331305/SRX331305.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:33:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331305/SRX331305.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:33:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331305/SRX331305.10_summits.bed INFO @ Tue, 16 Jun 2020 08:33:18: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (181 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:33:19: 1000000 INFO @ Tue, 16 Jun 2020 08:33:24: 2000000 INFO @ Tue, 16 Jun 2020 08:33:29: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:33:34: 4000000 INFO @ Tue, 16 Jun 2020 08:33:34: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:33:34: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:33:34: #1 total tags in treatment: 4157513 INFO @ Tue, 16 Jun 2020 08:33:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:33:34: #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 08:33:35: #1 tags after filtering in treatment: 4157513 INFO @ Tue, 16 Jun 2020 08:33:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:33:35: #1 finished! INFO @ Tue, 16 Jun 2020 08:33:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:33:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:33:35: #2 number of paired peaks: 381 WARNING @ Tue, 16 Jun 2020 08:33:35: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Tue, 16 Jun 2020 08:33:35: start model_add_line... INFO @ Tue, 16 Jun 2020 08:33:35: start X-correlation... INFO @ Tue, 16 Jun 2020 08:33:35: end of X-cor INFO @ Tue, 16 Jun 2020 08:33:35: #2 finished! INFO @ Tue, 16 Jun 2020 08:33:35: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 08:33:35: #2 alternative fragment length(s) may be 4,38,411 bps INFO @ Tue, 16 Jun 2020 08:33:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331305/SRX331305.20_model.r WARNING @ Tue, 16 Jun 2020 08:33:35: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:33:35: #2 You may need to consider one of the other alternative d(s): 4,38,411 WARNING @ Tue, 16 Jun 2020 08:33:35: #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 08:33:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:33:35: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:33:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:33:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331305/SRX331305.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:33:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331305/SRX331305.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:33:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331305/SRX331305.20_summits.bed INFO @ Tue, 16 Jun 2020 08:33:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (64 records, 4 fields): 1 millis CompletedMACS2peakCalling