Job ID = 6455052 SRX = SRX2642399 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:53:10 prefetch.2.10.7: 1) Downloading 'SRR5345739'... 2020-06-21T09:53:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:54:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:54:05 prefetch.2.10.7: 'SRR5345739' is valid 2020-06-21T09:54:05 prefetch.2.10.7: 1) 'SRR5345739' was downloaded successfully 2020-06-21T09:54:05 prefetch.2.10.7: 'SRR5345739' has 0 unresolved dependencies Read 3401169 spots for SRR5345739/SRR5345739.sra Written 3401169 spots for SRR5345739/SRR5345739.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: 00:01:26 3401169 reads; of these: 3401169 (100.00%) were unpaired; of these: 628895 (18.49%) aligned 0 times 2080836 (61.18%) aligned exactly 1 time 691438 (20.33%) aligned >1 times 81.51% overall alignment rate Time searching: 00:01:26 Overall time: 00:01:26 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 97449 / 2772274 = 0.0352 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 @ Sun, 21 Jun 2020 18:57:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642399/SRX2642399.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642399/SRX2642399.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642399/SRX2642399.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642399/SRX2642399.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 18:57:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:57:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:57:26: 1000000 INFO @ Sun, 21 Jun 2020 18:57:33: 2000000 INFO @ Sun, 21 Jun 2020 18:57:39: #1 tag size is determined as 92 bps INFO @ Sun, 21 Jun 2020 18:57:39: #1 tag size = 92 INFO @ Sun, 21 Jun 2020 18:57:39: #1 total tags in treatment: 2674825 INFO @ Sun, 21 Jun 2020 18:57:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:57:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:57:39: #1 tags after filtering in treatment: 2674785 INFO @ Sun, 21 Jun 2020 18:57:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:57:39: #1 finished! INFO @ Sun, 21 Jun 2020 18:57:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:57:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:57:40: #2 number of paired peaks: 490 WARNING @ Sun, 21 Jun 2020 18:57:40: Fewer paired peaks (490) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 490 pairs to build model! INFO @ Sun, 21 Jun 2020 18:57:40: start model_add_line... INFO @ Sun, 21 Jun 2020 18:57:40: start X-correlation... INFO @ Sun, 21 Jun 2020 18:57:40: end of X-cor INFO @ Sun, 21 Jun 2020 18:57:40: #2 finished! INFO @ Sun, 21 Jun 2020 18:57:40: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 18:57:40: #2 alternative fragment length(s) may be 91,492 bps INFO @ Sun, 21 Jun 2020 18:57:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642399/SRX2642399.05_model.r WARNING @ Sun, 21 Jun 2020 18:57:40: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:57:40: #2 You may need to consider one of the other alternative d(s): 91,492 WARNING @ Sun, 21 Jun 2020 18:57:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:57:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:57:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:57:46: #3 Call peaks for each chromosome... 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 @ Sun, 21 Jun 2020 18:57:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642399/SRX2642399.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642399/SRX2642399.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642399/SRX2642399.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642399/SRX2642399.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 18:57:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:57:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:57:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642399/SRX2642399.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:57:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642399/SRX2642399.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:57:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642399/SRX2642399.05_summits.bed INFO @ Sun, 21 Jun 2020 18:57:49: Done! pass1 - making usageList (419 chroms): 1 millis pass2 - checking and writing primary data (791 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:57:56: 1000000 INFO @ Sun, 21 Jun 2020 18:58:04: 2000000 INFO @ Sun, 21 Jun 2020 18:58:09: #1 tag size is determined as 92 bps INFO @ Sun, 21 Jun 2020 18:58:09: #1 tag size = 92 INFO @ Sun, 21 Jun 2020 18:58:09: #1 total tags in treatment: 2674825 INFO @ Sun, 21 Jun 2020 18:58:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:58:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:58:10: #1 tags after filtering in treatment: 2674785 INFO @ Sun, 21 Jun 2020 18:58:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:58:10: #1 finished! INFO @ Sun, 21 Jun 2020 18:58:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:58:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:58:10: #2 number of paired peaks: 490 WARNING @ Sun, 21 Jun 2020 18:58:10: Fewer paired peaks (490) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 490 pairs to build model! INFO @ Sun, 21 Jun 2020 18:58:10: start model_add_line... INFO @ Sun, 21 Jun 2020 18:58:10: start X-correlation... INFO @ Sun, 21 Jun 2020 18:58:10: end of X-cor INFO @ Sun, 21 Jun 2020 18:58:10: #2 finished! INFO @ Sun, 21 Jun 2020 18:58:10: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 18:58:10: #2 alternative fragment length(s) may be 91,492 bps INFO @ Sun, 21 Jun 2020 18:58:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642399/SRX2642399.10_model.r WARNING @ Sun, 21 Jun 2020 18:58:10: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:58:10: #2 You may need to consider one of the other alternative d(s): 91,492 WARNING @ Sun, 21 Jun 2020 18:58:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:58:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:58:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:58:16: #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 @ Sun, 21 Jun 2020 18:58:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642399/SRX2642399.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642399/SRX2642399.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642399/SRX2642399.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642399/SRX2642399.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 18:58:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:58:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:58:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642399/SRX2642399.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:58:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642399/SRX2642399.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:58:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642399/SRX2642399.10_summits.bed INFO @ Sun, 21 Jun 2020 18:58:19: Done! pass1 - making usageList (235 chroms): 1 millis pass2 - checking and writing primary data (374 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:58:26: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:58:34: 2000000 INFO @ Sun, 21 Jun 2020 18:58:40: #1 tag size is determined as 92 bps INFO @ Sun, 21 Jun 2020 18:58:40: #1 tag size = 92 INFO @ Sun, 21 Jun 2020 18:58:40: #1 total tags in treatment: 2674825 INFO @ Sun, 21 Jun 2020 18:58:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:58:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:58:40: #1 tags after filtering in treatment: 2674785 INFO @ Sun, 21 Jun 2020 18:58:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:58:40: #1 finished! INFO @ Sun, 21 Jun 2020 18:58:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:58:40: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:58:40: #2 number of paired peaks: 490 WARNING @ Sun, 21 Jun 2020 18:58:40: Fewer paired peaks (490) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 490 pairs to build model! INFO @ Sun, 21 Jun 2020 18:58:40: start model_add_line... INFO @ Sun, 21 Jun 2020 18:58:40: start X-correlation... INFO @ Sun, 21 Jun 2020 18:58:40: end of X-cor INFO @ Sun, 21 Jun 2020 18:58:40: #2 finished! INFO @ Sun, 21 Jun 2020 18:58:40: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 18:58:40: #2 alternative fragment length(s) may be 91,492 bps INFO @ Sun, 21 Jun 2020 18:58:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642399/SRX2642399.20_model.r WARNING @ Sun, 21 Jun 2020 18:58:40: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:58:40: #2 You may need to consider one of the other alternative d(s): 91,492 WARNING @ Sun, 21 Jun 2020 18:58:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:58:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:58:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:58:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:58:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642399/SRX2642399.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:58:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642399/SRX2642399.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:58:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642399/SRX2642399.20_summits.bed INFO @ Sun, 21 Jun 2020 18:58:49: Done! pass1 - making usageList (117 chroms): 1 millis pass2 - checking and writing primary data (164 records, 4 fields): 4 millis CompletedMACS2peakCalling