Job ID = 6365836 SRX = ERX1999207 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:13:42 prefetch.2.10.7: 1) Downloading 'ERR1938674'... 2020-06-15T22:13:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:14:21 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:14:21 prefetch.2.10.7: 'ERR1938674' is valid 2020-06-15T22:14:21 prefetch.2.10.7: 1) 'ERR1938674' was downloaded successfully Read 7622465 spots for ERR1938674/ERR1938674.sra Written 7622465 spots for ERR1938674/ERR1938674.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: 00:00:01 Multiseed full-index search: 00:01:23 7622465 reads; of these: 7622465 (100.00%) were unpaired; of these: 3503507 (45.96%) aligned 0 times 3167418 (41.55%) aligned exactly 1 time 951540 (12.48%) aligned >1 times 54.04% overall alignment rate Time searching: 00:01:24 Overall time: 00:01:24 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] 965642 / 4118958 = 0.2344 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 07:17:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/ERX1999207/ERX1999207.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/ERX1999207/ERX1999207.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/ERX1999207/ERX1999207.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/ERX1999207/ERX1999207.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 07:17:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:17:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:17:39: 1000000 INFO @ Tue, 16 Jun 2020 07:17:45: 2000000 INFO @ Tue, 16 Jun 2020 07:17:51: 3000000 INFO @ Tue, 16 Jun 2020 07:17:52: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 07:17:52: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 07:17:52: #1 total tags in treatment: 3153316 INFO @ Tue, 16 Jun 2020 07:17:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:17:52: #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 07:17:52: #1 tags after filtering in treatment: 3153316 INFO @ Tue, 16 Jun 2020 07:17:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:17:52: #1 finished! INFO @ Tue, 16 Jun 2020 07:17:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:17:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:17:53: #2 number of paired peaks: 460 WARNING @ Tue, 16 Jun 2020 07:17:53: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Tue, 16 Jun 2020 07:17:53: start model_add_line... INFO @ Tue, 16 Jun 2020 07:17:53: start X-correlation... INFO @ Tue, 16 Jun 2020 07:17:53: end of X-cor INFO @ Tue, 16 Jun 2020 07:17:53: #2 finished! INFO @ Tue, 16 Jun 2020 07:17:53: #2 predicted fragment length is 59 bps INFO @ Tue, 16 Jun 2020 07:17:53: #2 alternative fragment length(s) may be 4,59,84 bps INFO @ Tue, 16 Jun 2020 07:17:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/ERX1999207/ERX1999207.05_model.r WARNING @ Tue, 16 Jun 2020 07:17:53: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:17:53: #2 You may need to consider one of the other alternative d(s): 4,59,84 WARNING @ Tue, 16 Jun 2020 07:17:53: #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 07:17:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:17:53: #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 07:18:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:18:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/ERX1999207/ERX1999207.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/ERX1999207/ERX1999207.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/ERX1999207/ERX1999207.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/ERX1999207/ERX1999207.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 07:18:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:18:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:18:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/ERX1999207/ERX1999207.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:18:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/ERX1999207/ERX1999207.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:18:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/ERX1999207/ERX1999207.05_summits.bed INFO @ Tue, 16 Jun 2020 07:18:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (556 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:18:09: 1000000 INFO @ Tue, 16 Jun 2020 07:18:15: 2000000 INFO @ Tue, 16 Jun 2020 07:18:21: 3000000 INFO @ Tue, 16 Jun 2020 07:18:22: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 07:18:22: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 07:18:22: #1 total tags in treatment: 3153316 INFO @ Tue, 16 Jun 2020 07:18:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:18:22: #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 07:18:22: #1 tags after filtering in treatment: 3153316 INFO @ Tue, 16 Jun 2020 07:18:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:18:22: #1 finished! INFO @ Tue, 16 Jun 2020 07:18:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:18:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:18:23: #2 number of paired peaks: 460 WARNING @ Tue, 16 Jun 2020 07:18:23: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Tue, 16 Jun 2020 07:18:23: start model_add_line... INFO @ Tue, 16 Jun 2020 07:18:23: start X-correlation... INFO @ Tue, 16 Jun 2020 07:18:23: end of X-cor INFO @ Tue, 16 Jun 2020 07:18:23: #2 finished! INFO @ Tue, 16 Jun 2020 07:18:23: #2 predicted fragment length is 59 bps INFO @ Tue, 16 Jun 2020 07:18:23: #2 alternative fragment length(s) may be 4,59,84 bps INFO @ Tue, 16 Jun 2020 07:18:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/ERX1999207/ERX1999207.10_model.r WARNING @ Tue, 16 Jun 2020 07:18:23: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:18:23: #2 You may need to consider one of the other alternative d(s): 4,59,84 WARNING @ Tue, 16 Jun 2020 07:18:23: #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 07:18:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:18:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:18:30: #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 07:18:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/ERX1999207/ERX1999207.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/ERX1999207/ERX1999207.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/ERX1999207/ERX1999207.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/ERX1999207/ERX1999207.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 07:18:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:18:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:18:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/ERX1999207/ERX1999207.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:18:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/ERX1999207/ERX1999207.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:18:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/ERX1999207/ERX1999207.10_summits.bed INFO @ Tue, 16 Jun 2020 07:18:34: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (134 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:18:39: 1000000 INFO @ Tue, 16 Jun 2020 07:18:45: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:18:52: 3000000 INFO @ Tue, 16 Jun 2020 07:18:53: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 07:18:53: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 07:18:53: #1 total tags in treatment: 3153316 INFO @ Tue, 16 Jun 2020 07:18:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:18:53: #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 07:18:53: #1 tags after filtering in treatment: 3153316 INFO @ Tue, 16 Jun 2020 07:18:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:18:53: #1 finished! INFO @ Tue, 16 Jun 2020 07:18:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:18:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:18:53: #2 number of paired peaks: 460 WARNING @ Tue, 16 Jun 2020 07:18:53: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Tue, 16 Jun 2020 07:18:53: start model_add_line... INFO @ Tue, 16 Jun 2020 07:18:53: start X-correlation... INFO @ Tue, 16 Jun 2020 07:18:53: end of X-cor INFO @ Tue, 16 Jun 2020 07:18:53: #2 finished! INFO @ Tue, 16 Jun 2020 07:18:53: #2 predicted fragment length is 59 bps INFO @ Tue, 16 Jun 2020 07:18:53: #2 alternative fragment length(s) may be 4,59,84 bps INFO @ Tue, 16 Jun 2020 07:18:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/ERX1999207/ERX1999207.20_model.r WARNING @ Tue, 16 Jun 2020 07:18:53: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:18:53: #2 You may need to consider one of the other alternative d(s): 4,59,84 WARNING @ Tue, 16 Jun 2020 07:18:53: #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 07:18:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:18:53: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:19:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:19:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/ERX1999207/ERX1999207.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:19:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/ERX1999207/ERX1999207.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:19:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/ERX1999207/ERX1999207.20_summits.bed INFO @ Tue, 16 Jun 2020 07:19:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (50 records, 4 fields): 1 millis CompletedMACS2peakCalling