Job ID = 6365957 SRX = SRX043969 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:36:06 prefetch.2.10.7: 1) Downloading 'SRR107544'... 2020-06-15T22:36:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:36:30 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:36:30 prefetch.2.10.7: 'SRR107544' is valid 2020-06-15T22:36:30 prefetch.2.10.7: 1) 'SRR107544' was downloaded successfully Read 3528845 spots for SRR107544/SRR107544.sra Written 3528845 spots for SRR107544/SRR107544.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: 00:00:32 3528845 reads; of these: 3528845 (100.00%) were unpaired; of these: 1132891 (32.10%) aligned 0 times 2066832 (58.57%) aligned exactly 1 time 329122 (9.33%) aligned >1 times 67.90% overall alignment rate Time searching: 00:00:32 Overall time: 00:00:32 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] 138335 / 2395954 = 0.0577 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 07:38:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043969/SRX043969.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043969/SRX043969.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043969/SRX043969.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043969/SRX043969.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 07:38:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:38:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:38:28: 1000000 INFO @ Tue, 16 Jun 2020 07:38:33: 2000000 INFO @ Tue, 16 Jun 2020 07:38:34: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:38:34: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:38:34: #1 total tags in treatment: 2257619 INFO @ Tue, 16 Jun 2020 07:38:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:38:34: #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 07:38:35: #1 tags after filtering in treatment: 2257619 INFO @ Tue, 16 Jun 2020 07:38:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:38:35: #1 finished! INFO @ Tue, 16 Jun 2020 07:38:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:38:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:38:35: #2 number of paired peaks: 270 WARNING @ Tue, 16 Jun 2020 07:38:35: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Tue, 16 Jun 2020 07:38:35: start model_add_line... INFO @ Tue, 16 Jun 2020 07:38:35: start X-correlation... INFO @ Tue, 16 Jun 2020 07:38:35: end of X-cor INFO @ Tue, 16 Jun 2020 07:38:35: #2 finished! INFO @ Tue, 16 Jun 2020 07:38:35: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 07:38:35: #2 alternative fragment length(s) may be 2,39,584 bps INFO @ Tue, 16 Jun 2020 07:38:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043969/SRX043969.05_model.r WARNING @ Tue, 16 Jun 2020 07:38:35: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:38:35: #2 You may need to consider one of the other alternative d(s): 2,39,584 WARNING @ Tue, 16 Jun 2020 07:38:35: #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 07:38:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:38:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:38:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:38:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043969/SRX043969.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:38:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043969/SRX043969.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:38:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043969/SRX043969.05_summits.bed INFO @ Tue, 16 Jun 2020 07:38:43: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (226 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 07:38:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043969/SRX043969.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043969/SRX043969.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043969/SRX043969.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043969/SRX043969.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 07:38:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:38:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:38:59: 1000000 INFO @ Tue, 16 Jun 2020 07:39:04: 2000000 INFO @ Tue, 16 Jun 2020 07:39:05: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:39:05: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:39:05: #1 total tags in treatment: 2257619 INFO @ Tue, 16 Jun 2020 07:39:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:39:05: #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 07:39:05: #1 tags after filtering in treatment: 2257619 INFO @ Tue, 16 Jun 2020 07:39:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:39:05: #1 finished! INFO @ Tue, 16 Jun 2020 07:39:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:39:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:39:06: #2 number of paired peaks: 270 WARNING @ Tue, 16 Jun 2020 07:39:06: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Tue, 16 Jun 2020 07:39:06: start model_add_line... INFO @ Tue, 16 Jun 2020 07:39:06: start X-correlation... INFO @ Tue, 16 Jun 2020 07:39:06: end of X-cor INFO @ Tue, 16 Jun 2020 07:39:06: #2 finished! INFO @ Tue, 16 Jun 2020 07:39:06: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 07:39:06: #2 alternative fragment length(s) may be 2,39,584 bps INFO @ Tue, 16 Jun 2020 07:39:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043969/SRX043969.10_model.r WARNING @ Tue, 16 Jun 2020 07:39:06: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:39:06: #2 You may need to consider one of the other alternative d(s): 2,39,584 WARNING @ Tue, 16 Jun 2020 07:39:06: #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 07:39:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:39:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:39:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:39:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043969/SRX043969.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:39:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043969/SRX043969.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:39:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043969/SRX043969.10_summits.bed INFO @ Tue, 16 Jun 2020 07:39:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (85 records, 4 fields): 0 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 07:39:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043969/SRX043969.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043969/SRX043969.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043969/SRX043969.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043969/SRX043969.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 07:39:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:39:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:39:28: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:39:34: 2000000 INFO @ Tue, 16 Jun 2020 07:39:35: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:39:35: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:39:35: #1 total tags in treatment: 2257619 INFO @ Tue, 16 Jun 2020 07:39:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:39:35: #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 07:39:35: #1 tags after filtering in treatment: 2257619 INFO @ Tue, 16 Jun 2020 07:39:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:39:35: #1 finished! INFO @ Tue, 16 Jun 2020 07:39:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:39:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:39:36: #2 number of paired peaks: 270 WARNING @ Tue, 16 Jun 2020 07:39:36: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Tue, 16 Jun 2020 07:39:36: start model_add_line... INFO @ Tue, 16 Jun 2020 07:39:36: start X-correlation... INFO @ Tue, 16 Jun 2020 07:39:36: end of X-cor INFO @ Tue, 16 Jun 2020 07:39:36: #2 finished! INFO @ Tue, 16 Jun 2020 07:39:36: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 07:39:36: #2 alternative fragment length(s) may be 2,39,584 bps INFO @ Tue, 16 Jun 2020 07:39:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043969/SRX043969.20_model.r WARNING @ Tue, 16 Jun 2020 07:39:36: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:39:36: #2 You may need to consider one of the other alternative d(s): 2,39,584 WARNING @ Tue, 16 Jun 2020 07:39:36: #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 07:39:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:39:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:39:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:39:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043969/SRX043969.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:39:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043969/SRX043969.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:39:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043969/SRX043969.20_summits.bed INFO @ Tue, 16 Jun 2020 07:39:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (12 records, 4 fields): 1 millis CompletedMACS2peakCalling