Job ID = 6367482 SRX = SRX331239 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:25:16 prefetch.2.10.7: 1) Downloading 'SRR947471'... 2020-06-15T23:25:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:26:03 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:26:03 prefetch.2.10.7: 'SRR947471' is valid 2020-06-15T23:26:03 prefetch.2.10.7: 1) 'SRR947471' was downloaded successfully Read 7203627 spots for SRR947471/SRR947471.sra Written 7203627 spots for SRR947471/SRR947471.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: 00:01:14 7203627 reads; of these: 7203627 (100.00%) were unpaired; of these: 163334 (2.27%) aligned 0 times 5873839 (81.54%) aligned exactly 1 time 1166454 (16.19%) aligned >1 times 97.73% overall alignment rate Time searching: 00:01:14 Overall time: 00:01:14 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_rmdupse_core] 843378 / 7040293 = 0.1198 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 08:29:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331239/SRX331239.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331239/SRX331239.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331239/SRX331239.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331239/SRX331239.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 08:29:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:29:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:29:34: 1000000 INFO @ Tue, 16 Jun 2020 08:29:39: 2000000 INFO @ Tue, 16 Jun 2020 08:29:45: 3000000 INFO @ Tue, 16 Jun 2020 08:29:51: 4000000 INFO @ Tue, 16 Jun 2020 08:29:56: 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 @ Tue, 16 Jun 2020 08:29:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331239/SRX331239.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331239/SRX331239.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331239/SRX331239.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331239/SRX331239.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 08:29:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:29:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:30:02: 6000000 INFO @ Tue, 16 Jun 2020 08:30:03: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:30:03: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:30:03: #1 total tags in treatment: 6196915 INFO @ Tue, 16 Jun 2020 08:30:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:30:03: #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 08:30:03: #1 tags after filtering in treatment: 6196915 INFO @ Tue, 16 Jun 2020 08:30:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:30:03: #1 finished! INFO @ Tue, 16 Jun 2020 08:30:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:30:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:30:04: #2 number of paired peaks: 376 WARNING @ Tue, 16 Jun 2020 08:30:04: Fewer paired peaks (376) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 376 pairs to build model! INFO @ Tue, 16 Jun 2020 08:30:04: start model_add_line... INFO @ Tue, 16 Jun 2020 08:30:04: start X-correlation... INFO @ Tue, 16 Jun 2020 08:30:04: end of X-cor INFO @ Tue, 16 Jun 2020 08:30:04: #2 finished! INFO @ Tue, 16 Jun 2020 08:30:04: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:30:04: #2 alternative fragment length(s) may be 2,31,85,575 bps INFO @ Tue, 16 Jun 2020 08:30:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331239/SRX331239.05_model.r WARNING @ Tue, 16 Jun 2020 08:30:04: #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 08:30:04: #2 You may need to consider one of the other alternative d(s): 2,31,85,575 WARNING @ Tue, 16 Jun 2020 08:30:04: #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 08:30:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:30:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:30:05: 1000000 INFO @ Tue, 16 Jun 2020 08:30:11: 2000000 INFO @ Tue, 16 Jun 2020 08:30:18: 3000000 INFO @ Tue, 16 Jun 2020 08:30:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:30:24: 4000000 INFO @ Tue, 16 Jun 2020 08:30:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331239/SRX331239.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:30:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331239/SRX331239.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:30:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331239/SRX331239.05_summits.bed INFO @ Tue, 16 Jun 2020 08:30:25: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (410 records, 4 fields): 2 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 08:30:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331239/SRX331239.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331239/SRX331239.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331239/SRX331239.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331239/SRX331239.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 08:30:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:30:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:30:30: 5000000 INFO @ Tue, 16 Jun 2020 08:30:34: 1000000 INFO @ Tue, 16 Jun 2020 08:30:37: 6000000 INFO @ Tue, 16 Jun 2020 08:30:38: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:30:38: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:30:38: #1 total tags in treatment: 6196915 INFO @ Tue, 16 Jun 2020 08:30:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:30:38: #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 08:30:38: #1 tags after filtering in treatment: 6196915 INFO @ Tue, 16 Jun 2020 08:30:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:30:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:30:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:30:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:30:39: #2 number of paired peaks: 376 WARNING @ Tue, 16 Jun 2020 08:30:39: Fewer paired peaks (376) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 376 pairs to build model! INFO @ Tue, 16 Jun 2020 08:30:39: start model_add_line... INFO @ Tue, 16 Jun 2020 08:30:39: start X-correlation... INFO @ Tue, 16 Jun 2020 08:30:39: end of X-cor INFO @ Tue, 16 Jun 2020 08:30:39: #2 finished! INFO @ Tue, 16 Jun 2020 08:30:39: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:30:39: #2 alternative fragment length(s) may be 2,31,85,575 bps INFO @ Tue, 16 Jun 2020 08:30:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331239/SRX331239.10_model.r WARNING @ Tue, 16 Jun 2020 08:30:39: #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 08:30:39: #2 You may need to consider one of the other alternative d(s): 2,31,85,575 WARNING @ Tue, 16 Jun 2020 08:30:39: #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 08:30:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:30:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:30:40: 2000000 INFO @ Tue, 16 Jun 2020 08:30:46: 3000000 INFO @ Tue, 16 Jun 2020 08:30:51: 4000000 INFO @ Tue, 16 Jun 2020 08:30:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:30:57: 5000000 INFO @ Tue, 16 Jun 2020 08:30:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331239/SRX331239.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:30:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331239/SRX331239.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:30:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331239/SRX331239.10_summits.bed INFO @ Tue, 16 Jun 2020 08:30:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (196 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:31:02: 6000000 INFO @ Tue, 16 Jun 2020 08:31:03: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:31:03: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:31:03: #1 total tags in treatment: 6196915 INFO @ Tue, 16 Jun 2020 08:31:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:31:03: #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 08:31:03: #1 tags after filtering in treatment: 6196915 INFO @ Tue, 16 Jun 2020 08:31:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:31:03: #1 finished! INFO @ Tue, 16 Jun 2020 08:31:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:31:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:31:04: #2 number of paired peaks: 376 WARNING @ Tue, 16 Jun 2020 08:31:04: Fewer paired peaks (376) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 376 pairs to build model! INFO @ Tue, 16 Jun 2020 08:31:04: start model_add_line... INFO @ Tue, 16 Jun 2020 08:31:04: start X-correlation... INFO @ Tue, 16 Jun 2020 08:31:04: end of X-cor INFO @ Tue, 16 Jun 2020 08:31:04: #2 finished! INFO @ Tue, 16 Jun 2020 08:31:04: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:31:04: #2 alternative fragment length(s) may be 2,31,85,575 bps INFO @ Tue, 16 Jun 2020 08:31:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331239/SRX331239.20_model.r WARNING @ Tue, 16 Jun 2020 08:31:04: #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 08:31:04: #2 You may need to consider one of the other alternative d(s): 2,31,85,575 WARNING @ Tue, 16 Jun 2020 08:31:04: #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 08:31:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:31:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:31:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:31:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331239/SRX331239.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:31:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331239/SRX331239.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:31:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331239/SRX331239.20_summits.bed INFO @ Tue, 16 Jun 2020 08:31:24: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (32 records, 4 fields): 1 millis CompletedMACS2peakCalling