Job ID = 6367474 SRX = SRX331231 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:44:44 prefetch.2.10.7: 1) Downloading 'SRR947463'... 2020-06-15T23:44:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:45:38 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:45:39 prefetch.2.10.7: 'SRR947463' is valid 2020-06-15T23:45:39 prefetch.2.10.7: 1) 'SRR947463' was downloaded successfully Read 7491366 spots for SRR947463/SRR947463.sra Written 7491366 spots for SRR947463/SRR947463.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: 00:01:08 7491366 reads; of these: 7491366 (100.00%) were unpaired; of these: 99241 (1.32%) aligned 0 times 6266856 (83.65%) aligned exactly 1 time 1125269 (15.02%) aligned >1 times 98.68% overall alignment rate Time searching: 00:01:08 Overall time: 00:01:08 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] 652825 / 7392125 = 0.0883 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 08:48:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331231/SRX331231.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331231/SRX331231.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331231/SRX331231.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331231/SRX331231.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 08:48:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:48:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:01: 1000000 INFO @ Tue, 16 Jun 2020 08:49:06: 2000000 INFO @ Tue, 16 Jun 2020 08:49:12: 3000000 INFO @ Tue, 16 Jun 2020 08:49:17: 4000000 INFO @ Tue, 16 Jun 2020 08:49:22: 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 08:49:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331231/SRX331231.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331231/SRX331231.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331231/SRX331231.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331231/SRX331231.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 08:49:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:27: 6000000 INFO @ Tue, 16 Jun 2020 08:49:31: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:49:31: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:49:31: #1 total tags in treatment: 6739300 INFO @ Tue, 16 Jun 2020 08:49:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:49:31: #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 08:49:31: 1000000 INFO @ Tue, 16 Jun 2020 08:49:31: #1 tags after filtering in treatment: 6739300 INFO @ Tue, 16 Jun 2020 08:49:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:49:31: #1 finished! INFO @ Tue, 16 Jun 2020 08:49:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:49:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:49:32: #2 number of paired peaks: 399 WARNING @ Tue, 16 Jun 2020 08:49:32: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Tue, 16 Jun 2020 08:49:32: start model_add_line... INFO @ Tue, 16 Jun 2020 08:49:32: start X-correlation... INFO @ Tue, 16 Jun 2020 08:49:32: end of X-cor INFO @ Tue, 16 Jun 2020 08:49:32: #2 finished! INFO @ Tue, 16 Jun 2020 08:49:32: #2 predicted fragment length is 29 bps INFO @ Tue, 16 Jun 2020 08:49:32: #2 alternative fragment length(s) may be 2,29,78,540,580 bps INFO @ Tue, 16 Jun 2020 08:49:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331231/SRX331231.05_model.r WARNING @ Tue, 16 Jun 2020 08:49:32: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:49:32: #2 You may need to consider one of the other alternative d(s): 2,29,78,540,580 WARNING @ Tue, 16 Jun 2020 08:49:32: #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 08:49:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:49:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:49:37: 2000000 INFO @ Tue, 16 Jun 2020 08:49:43: 3000000 INFO @ Tue, 16 Jun 2020 08:49:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:49:48: 4000000 INFO @ Tue, 16 Jun 2020 08:49:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331231/SRX331231.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:49:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331231/SRX331231.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:49:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331231/SRX331231.05_summits.bed INFO @ Tue, 16 Jun 2020 08:49:52: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (484 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:49:53: 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 @ Tue, 16 Jun 2020 08:49:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331231/SRX331231.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331231/SRX331231.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331231/SRX331231.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331231/SRX331231.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 08:49:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:59: 6000000 INFO @ Tue, 16 Jun 2020 08:50:01: 1000000 INFO @ Tue, 16 Jun 2020 08:50:03: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:50:03: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:50:03: #1 total tags in treatment: 6739300 INFO @ Tue, 16 Jun 2020 08:50:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:03: #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 08:50:03: #1 tags after filtering in treatment: 6739300 INFO @ Tue, 16 Jun 2020 08:50:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:03: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:04: #2 number of paired peaks: 399 WARNING @ Tue, 16 Jun 2020 08:50:04: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Tue, 16 Jun 2020 08:50:04: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:04: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:04: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:04: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:04: #2 predicted fragment length is 29 bps INFO @ Tue, 16 Jun 2020 08:50:04: #2 alternative fragment length(s) may be 2,29,78,540,580 bps INFO @ Tue, 16 Jun 2020 08:50:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331231/SRX331231.10_model.r WARNING @ Tue, 16 Jun 2020 08:50:04: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:50:04: #2 You may need to consider one of the other alternative d(s): 2,29,78,540,580 WARNING @ Tue, 16 Jun 2020 08:50:04: #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 08:50:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:50:07: 2000000 INFO @ Tue, 16 Jun 2020 08:50:12: 3000000 INFO @ Tue, 16 Jun 2020 08:50:17: 4000000 INFO @ Tue, 16 Jun 2020 08:50:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:50:22: 5000000 INFO @ Tue, 16 Jun 2020 08:50:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331231/SRX331231.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:50:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331231/SRX331231.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:50:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331231/SRX331231.10_summits.bed INFO @ Tue, 16 Jun 2020 08:50:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (192 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:50:27: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:50:31: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:50:31: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:50:31: #1 total tags in treatment: 6739300 INFO @ Tue, 16 Jun 2020 08:50:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:31: #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 08:50:31: #1 tags after filtering in treatment: 6739300 INFO @ Tue, 16 Jun 2020 08:50:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:31: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:32: #2 number of paired peaks: 399 WARNING @ Tue, 16 Jun 2020 08:50:32: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Tue, 16 Jun 2020 08:50:32: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:32: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:32: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:32: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:32: #2 predicted fragment length is 29 bps INFO @ Tue, 16 Jun 2020 08:50:32: #2 alternative fragment length(s) may be 2,29,78,540,580 bps INFO @ Tue, 16 Jun 2020 08:50:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331231/SRX331231.20_model.r WARNING @ Tue, 16 Jun 2020 08:50:32: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:50:32: #2 You may need to consider one of the other alternative d(s): 2,29,78,540,580 WARNING @ Tue, 16 Jun 2020 08:50:32: #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 08:50:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:50:45: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:50:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331231/SRX331231.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:50:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331231/SRX331231.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:50:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331231/SRX331231.20_summits.bed INFO @ Tue, 16 Jun 2020 08:50:52: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (33 records, 4 fields): 1 millis CompletedMACS2peakCalling