Job ID = 6453989 SRX = SRX1760697 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:37:09 prefetch.2.10.7: 1) Downloading 'SRR3503054'... 2020-06-21T08:37:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:38:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:38:59 prefetch.2.10.7: 'SRR3503054' is valid 2020-06-21T08:38:59 prefetch.2.10.7: 1) 'SRR3503054' was downloaded successfully 2020-06-21T08:38:59 prefetch.2.10.7: 'SRR3503054' has 0 unresolved dependencies Read 5576426 spots for SRR3503054/SRR3503054.sra Written 5576426 spots for SRR3503054/SRR3503054.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: 00:04:34 5576426 reads; of these: 5576426 (100.00%) were unpaired; of these: 1852134 (33.21%) aligned 0 times 2723579 (48.84%) aligned exactly 1 time 1000713 (17.95%) aligned >1 times 66.79% overall alignment rate Time searching: 00:04:34 Overall time: 00:04:34 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] 128984 / 3724292 = 0.0346 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 17:46:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1760697/SRX1760697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1760697/SRX1760697.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1760697/SRX1760697.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1760697/SRX1760697.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 17:46:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:46:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:46:32: 1000000 INFO @ Sun, 21 Jun 2020 17:46:39: 2000000 INFO @ Sun, 21 Jun 2020 17:46:46: 3000000 INFO @ Sun, 21 Jun 2020 17:46:51: #1 tag size is determined as 151 bps INFO @ Sun, 21 Jun 2020 17:46:51: #1 tag size = 151 INFO @ Sun, 21 Jun 2020 17:46:51: #1 total tags in treatment: 3595308 INFO @ Sun, 21 Jun 2020 17:46:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:46:51: #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 17:46:51: #1 tags after filtering in treatment: 3595073 INFO @ Sun, 21 Jun 2020 17:46:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:46:51: #1 finished! INFO @ Sun, 21 Jun 2020 17:46:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:46:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:46:51: #2 number of paired peaks: 948 WARNING @ Sun, 21 Jun 2020 17:46:51: Fewer paired peaks (948) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 948 pairs to build model! INFO @ Sun, 21 Jun 2020 17:46:51: start model_add_line... INFO @ Sun, 21 Jun 2020 17:46:51: start X-correlation... INFO @ Sun, 21 Jun 2020 17:46:51: end of X-cor INFO @ Sun, 21 Jun 2020 17:46:51: #2 finished! INFO @ Sun, 21 Jun 2020 17:46:51: #2 predicted fragment length is 147 bps INFO @ Sun, 21 Jun 2020 17:46:51: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 21 Jun 2020 17:46:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1760697/SRX1760697.05_model.r WARNING @ Sun, 21 Jun 2020 17:46:51: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:46:51: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Sun, 21 Jun 2020 17:46:51: #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 17:46:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:46:51: #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 @ Sun, 21 Jun 2020 17:46:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1760697/SRX1760697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1760697/SRX1760697.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1760697/SRX1760697.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1760697/SRX1760697.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 17:46:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:46:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:47:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:47:03: 1000000 INFO @ Sun, 21 Jun 2020 17:47:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1760697/SRX1760697.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:47:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1760697/SRX1760697.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:47:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1760697/SRX1760697.05_summits.bed INFO @ Sun, 21 Jun 2020 17:47:04: Done! pass1 - making usageList (545 chroms): 1 millis pass2 - checking and writing primary data (1308 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:47:11: 2000000 INFO @ Sun, 21 Jun 2020 17:47:20: 3000000 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 17:47:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1760697/SRX1760697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1760697/SRX1760697.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1760697/SRX1760697.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1760697/SRX1760697.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 17:47:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:47:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:47:26: #1 tag size is determined as 151 bps INFO @ Sun, 21 Jun 2020 17:47:26: #1 tag size = 151 INFO @ Sun, 21 Jun 2020 17:47:26: #1 total tags in treatment: 3595308 INFO @ Sun, 21 Jun 2020 17:47:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:47:26: #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 17:47:26: #1 tags after filtering in treatment: 3595073 INFO @ Sun, 21 Jun 2020 17:47:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:47:26: #1 finished! INFO @ Sun, 21 Jun 2020 17:47:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:47:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:47:26: #2 number of paired peaks: 948 WARNING @ Sun, 21 Jun 2020 17:47:26: Fewer paired peaks (948) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 948 pairs to build model! INFO @ Sun, 21 Jun 2020 17:47:26: start model_add_line... INFO @ Sun, 21 Jun 2020 17:47:26: start X-correlation... INFO @ Sun, 21 Jun 2020 17:47:27: end of X-cor INFO @ Sun, 21 Jun 2020 17:47:27: #2 finished! INFO @ Sun, 21 Jun 2020 17:47:27: #2 predicted fragment length is 147 bps INFO @ Sun, 21 Jun 2020 17:47:27: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 21 Jun 2020 17:47:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1760697/SRX1760697.10_model.r WARNING @ Sun, 21 Jun 2020 17:47:27: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:47:27: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Sun, 21 Jun 2020 17:47:27: #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 17:47:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:47:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:47:32: 1000000 INFO @ Sun, 21 Jun 2020 17:47:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:47:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1760697/SRX1760697.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:47:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1760697/SRX1760697.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:47:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1760697/SRX1760697.10_summits.bed INFO @ Sun, 21 Jun 2020 17:47:39: Done! pass1 - making usageList (431 chroms): 1 millis pass2 - checking and writing primary data (847 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:47:41: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:47:49: 3000000 INFO @ Sun, 21 Jun 2020 17:47:54: #1 tag size is determined as 151 bps INFO @ Sun, 21 Jun 2020 17:47:54: #1 tag size = 151 INFO @ Sun, 21 Jun 2020 17:47:54: #1 total tags in treatment: 3595308 INFO @ Sun, 21 Jun 2020 17:47:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:47:54: #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 17:47:55: #1 tags after filtering in treatment: 3595073 INFO @ Sun, 21 Jun 2020 17:47:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:47:55: #1 finished! INFO @ Sun, 21 Jun 2020 17:47:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:47:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:47:55: #2 number of paired peaks: 948 WARNING @ Sun, 21 Jun 2020 17:47:55: Fewer paired peaks (948) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 948 pairs to build model! INFO @ Sun, 21 Jun 2020 17:47:55: start model_add_line... INFO @ Sun, 21 Jun 2020 17:47:55: start X-correlation... INFO @ Sun, 21 Jun 2020 17:47:55: end of X-cor INFO @ Sun, 21 Jun 2020 17:47:55: #2 finished! INFO @ Sun, 21 Jun 2020 17:47:55: #2 predicted fragment length is 147 bps INFO @ Sun, 21 Jun 2020 17:47:55: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 21 Jun 2020 17:47:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1760697/SRX1760697.20_model.r WARNING @ Sun, 21 Jun 2020 17:47:55: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:47:55: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Sun, 21 Jun 2020 17:47:55: #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 17:47:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:47:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:48:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:48:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1760697/SRX1760697.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:48:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1760697/SRX1760697.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:48:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1760697/SRX1760697.20_summits.bed INFO @ Sun, 21 Jun 2020 17:48:08: Done! pass1 - making usageList (299 chroms): 1 millis pass2 - checking and writing primary data (448 records, 4 fields): 10 millis CompletedMACS2peakCalling