Job ID = 6366781 SRX = SRX233446 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 'SRR701501'... 2020-06-15T23:12:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:13:06 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:13:06 prefetch.2.10.7: 'SRR701501' is valid 2020-06-15T23:13:06 prefetch.2.10.7: 1) 'SRR701501' was downloaded successfully Read 7490240 spots for SRR701501/SRR701501.sra Written 7490240 spots for SRR701501/SRR701501.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: 00:01:10 7490240 reads; of these: 7490240 (100.00%) were unpaired; of these: 948107 (12.66%) aligned 0 times 5429425 (72.49%) aligned exactly 1 time 1112708 (14.86%) aligned >1 times 87.34% overall alignment rate Time searching: 00:01:10 Overall time: 00:01:10 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] 464100 / 6542133 = 0.0709 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 08:16:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX233446/SRX233446.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX233446/SRX233446.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX233446/SRX233446.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX233446/SRX233446.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 08:16:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:16:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:17:00: 1000000 INFO @ Tue, 16 Jun 2020 08:17:07: 2000000 INFO @ Tue, 16 Jun 2020 08:17:15: 3000000 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 08:17:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX233446/SRX233446.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX233446/SRX233446.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX233446/SRX233446.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX233446/SRX233446.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 08:17:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:17:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:17:23: 4000000 INFO @ Tue, 16 Jun 2020 08:17:30: 5000000 INFO @ Tue, 16 Jun 2020 08:17:30: 1000000 INFO @ Tue, 16 Jun 2020 08:17:37: 6000000 INFO @ Tue, 16 Jun 2020 08:17:38: 2000000 INFO @ Tue, 16 Jun 2020 08:17:38: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:17:38: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:17:38: #1 total tags in treatment: 6078033 INFO @ Tue, 16 Jun 2020 08:17:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:17:38: #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 08:17:38: #1 tags after filtering in treatment: 6078033 INFO @ Tue, 16 Jun 2020 08:17:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:17:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:17:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:17:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:17:38: #2 number of paired peaks: 403 WARNING @ Tue, 16 Jun 2020 08:17:38: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Tue, 16 Jun 2020 08:17:38: start model_add_line... INFO @ Tue, 16 Jun 2020 08:17:38: start X-correlation... INFO @ Tue, 16 Jun 2020 08:17:38: end of X-cor INFO @ Tue, 16 Jun 2020 08:17:38: #2 finished! INFO @ Tue, 16 Jun 2020 08:17:38: #2 predicted fragment length is 29 bps INFO @ Tue, 16 Jun 2020 08:17:38: #2 alternative fragment length(s) may be 2,29,550 bps INFO @ Tue, 16 Jun 2020 08:17:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX233446/SRX233446.05_model.r WARNING @ Tue, 16 Jun 2020 08:17:39: #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 08:17:39: #2 You may need to consider one of the other alternative d(s): 2,29,550 WARNING @ Tue, 16 Jun 2020 08:17:39: #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 08:17:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:17:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:17:45: 3000000 INFO @ Tue, 16 Jun 2020 08:17:50: #3 Call peaks for each chromosome... 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 08:17:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX233446/SRX233446.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX233446/SRX233446.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX233446/SRX233446.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX233446/SRX233446.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 08:17:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:17:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:17:53: 4000000 INFO @ Tue, 16 Jun 2020 08:17:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX233446/SRX233446.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:17:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX233446/SRX233446.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:17:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX233446/SRX233446.05_summits.bed INFO @ Tue, 16 Jun 2020 08:17:56: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (574 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:18:00: 1000000 INFO @ Tue, 16 Jun 2020 08:18:01: 5000000 INFO @ Tue, 16 Jun 2020 08:18:08: 2000000 INFO @ Tue, 16 Jun 2020 08:18:08: 6000000 INFO @ Tue, 16 Jun 2020 08:18:08: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:18:08: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:18:08: #1 total tags in treatment: 6078033 INFO @ Tue, 16 Jun 2020 08:18:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:18:08: #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 08:18:08: #1 tags after filtering in treatment: 6078033 INFO @ Tue, 16 Jun 2020 08:18:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:18:08: #1 finished! INFO @ Tue, 16 Jun 2020 08:18:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:18:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:18:09: #2 number of paired peaks: 403 WARNING @ Tue, 16 Jun 2020 08:18:09: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Tue, 16 Jun 2020 08:18:09: start model_add_line... INFO @ Tue, 16 Jun 2020 08:18:09: start X-correlation... INFO @ Tue, 16 Jun 2020 08:18:09: end of X-cor INFO @ Tue, 16 Jun 2020 08:18:09: #2 finished! INFO @ Tue, 16 Jun 2020 08:18:09: #2 predicted fragment length is 29 bps INFO @ Tue, 16 Jun 2020 08:18:09: #2 alternative fragment length(s) may be 2,29,550 bps INFO @ Tue, 16 Jun 2020 08:18:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX233446/SRX233446.10_model.r WARNING @ Tue, 16 Jun 2020 08:18:09: #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 08:18:09: #2 You may need to consider one of the other alternative d(s): 2,29,550 WARNING @ Tue, 16 Jun 2020 08:18:09: #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 08:18:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:18:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:18:15: 3000000 INFO @ Tue, 16 Jun 2020 08:18:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:18:23: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:18:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX233446/SRX233446.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:18:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX233446/SRX233446.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:18:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX233446/SRX233446.10_summits.bed INFO @ Tue, 16 Jun 2020 08:18:26: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (297 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:18:30: 5000000 INFO @ Tue, 16 Jun 2020 08:18:38: 6000000 INFO @ Tue, 16 Jun 2020 08:18:38: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:18:38: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:18:38: #1 total tags in treatment: 6078033 INFO @ Tue, 16 Jun 2020 08:18:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:18:38: #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 08:18:39: #1 tags after filtering in treatment: 6078033 INFO @ Tue, 16 Jun 2020 08:18:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:18:39: #1 finished! INFO @ Tue, 16 Jun 2020 08:18:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:18:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:18:39: #2 number of paired peaks: 403 WARNING @ Tue, 16 Jun 2020 08:18:39: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Tue, 16 Jun 2020 08:18:39: start model_add_line... INFO @ Tue, 16 Jun 2020 08:18:39: start X-correlation... INFO @ Tue, 16 Jun 2020 08:18:39: end of X-cor INFO @ Tue, 16 Jun 2020 08:18:39: #2 finished! INFO @ Tue, 16 Jun 2020 08:18:39: #2 predicted fragment length is 29 bps INFO @ Tue, 16 Jun 2020 08:18:39: #2 alternative fragment length(s) may be 2,29,550 bps INFO @ Tue, 16 Jun 2020 08:18:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX233446/SRX233446.20_model.r WARNING @ Tue, 16 Jun 2020 08:18:39: #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 08:18:39: #2 You may need to consider one of the other alternative d(s): 2,29,550 WARNING @ Tue, 16 Jun 2020 08:18:39: #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 08:18:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:18:39: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:18:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:18:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX233446/SRX233446.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:18:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX233446/SRX233446.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:18:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX233446/SRX233446.20_summits.bed INFO @ Tue, 16 Jun 2020 08:18:57: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (74 records, 4 fields): 2 millis CompletedMACS2peakCalling