Job ID = 6458394 SRX = SRX511134 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:44:22 prefetch.2.10.7: 1) Downloading 'SRR1217239'... 2020-06-21T12:44:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:45:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:45:53 prefetch.2.10.7: 'SRR1217239' is valid 2020-06-21T12:45:53 prefetch.2.10.7: 1) 'SRR1217239' was downloaded successfully Read 7106315 spots for SRR1217239/SRR1217239.sra Written 7106315 spots for SRR1217239/SRR1217239.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: 00:02:14 7106315 reads; of these: 7106315 (100.00%) were unpaired; of these: 178628 (2.51%) aligned 0 times 4510504 (63.47%) aligned exactly 1 time 2417183 (34.01%) aligned >1 times 97.49% overall alignment rate Time searching: 00:02:15 Overall time: 00:02:15 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] 632974 / 6927687 = 0.0914 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 21:50:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX511134/SRX511134.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX511134/SRX511134.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX511134/SRX511134.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX511134/SRX511134.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 21:50:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:50:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:50:44: 1000000 INFO @ Sun, 21 Jun 2020 21:50:50: 2000000 INFO @ Sun, 21 Jun 2020 21:50:56: 3000000 INFO @ Sun, 21 Jun 2020 21:51:02: 4000000 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 21:51:07: 5000000 INFO @ Sun, 21 Jun 2020 21:51:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX511134/SRX511134.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX511134/SRX511134.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX511134/SRX511134.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX511134/SRX511134.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 21:51:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:51:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:51:14: 6000000 INFO @ Sun, 21 Jun 2020 21:51:15: 1000000 INFO @ Sun, 21 Jun 2020 21:51:16: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:51:16: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:51:16: #1 total tags in treatment: 6294713 INFO @ Sun, 21 Jun 2020 21:51:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:51:16: #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 21:51:16: #1 tags after filtering in treatment: 6294581 INFO @ Sun, 21 Jun 2020 21:51:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:51:16: #1 finished! INFO @ Sun, 21 Jun 2020 21:51:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:51:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:51:17: #2 number of paired peaks: 2436 INFO @ Sun, 21 Jun 2020 21:51:17: start model_add_line... INFO @ Sun, 21 Jun 2020 21:51:17: start X-correlation... INFO @ Sun, 21 Jun 2020 21:51:17: end of X-cor INFO @ Sun, 21 Jun 2020 21:51:17: #2 finished! INFO @ Sun, 21 Jun 2020 21:51:17: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 21:51:17: #2 alternative fragment length(s) may be 4,60 bps INFO @ Sun, 21 Jun 2020 21:51:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX511134/SRX511134.05_model.r WARNING @ Sun, 21 Jun 2020 21:51:17: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:51:17: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Sun, 21 Jun 2020 21:51:17: #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 21:51:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:51:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:51:21: 2000000 INFO @ Sun, 21 Jun 2020 21:51:27: 3000000 INFO @ Sun, 21 Jun 2020 21:51:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:51:33: 4000000 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 21:51:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX511134/SRX511134.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:51:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX511134/SRX511134.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:51:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX511134/SRX511134.05_summits.bed INFO @ Sun, 21 Jun 2020 21:51:38: Done! pass1 - making usageList (540 chroms): 2 millis pass2 - checking and writing primary data (2373 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:51:38: 5000000 INFO @ Sun, 21 Jun 2020 21:51:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX511134/SRX511134.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX511134/SRX511134.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX511134/SRX511134.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX511134/SRX511134.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 21:51:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:51:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:51:45: 1000000 INFO @ Sun, 21 Jun 2020 21:51:45: 6000000 INFO @ Sun, 21 Jun 2020 21:51:47: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:51:47: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:51:47: #1 total tags in treatment: 6294713 INFO @ Sun, 21 Jun 2020 21:51:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:51:47: #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 21:51:47: #1 tags after filtering in treatment: 6294581 INFO @ Sun, 21 Jun 2020 21:51:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:51:47: #1 finished! INFO @ Sun, 21 Jun 2020 21:51:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:51:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:51:48: #2 number of paired peaks: 2436 INFO @ Sun, 21 Jun 2020 21:51:48: start model_add_line... INFO @ Sun, 21 Jun 2020 21:51:48: start X-correlation... INFO @ Sun, 21 Jun 2020 21:51:48: end of X-cor INFO @ Sun, 21 Jun 2020 21:51:48: #2 finished! INFO @ Sun, 21 Jun 2020 21:51:48: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 21:51:48: #2 alternative fragment length(s) may be 4,60 bps INFO @ Sun, 21 Jun 2020 21:51:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX511134/SRX511134.10_model.r WARNING @ Sun, 21 Jun 2020 21:51:48: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:51:48: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Sun, 21 Jun 2020 21:51:48: #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 21:51:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:51:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:51:51: 2000000 INFO @ Sun, 21 Jun 2020 21:51:56: 3000000 INFO @ Sun, 21 Jun 2020 21:52:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:52:02: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:52:08: 5000000 INFO @ Sun, 21 Jun 2020 21:52:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX511134/SRX511134.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:52:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX511134/SRX511134.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:52:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX511134/SRX511134.10_summits.bed INFO @ Sun, 21 Jun 2020 21:52:09: Done! pass1 - making usageList (464 chroms): 1 millis pass2 - checking and writing primary data (1534 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:52:14: 6000000 INFO @ Sun, 21 Jun 2020 21:52:16: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:52:16: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:52:16: #1 total tags in treatment: 6294713 INFO @ Sun, 21 Jun 2020 21:52:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:52:16: #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 21:52:16: #1 tags after filtering in treatment: 6294581 INFO @ Sun, 21 Jun 2020 21:52:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:52:16: #1 finished! INFO @ Sun, 21 Jun 2020 21:52:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:52:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:52:17: #2 number of paired peaks: 2436 INFO @ Sun, 21 Jun 2020 21:52:17: start model_add_line... INFO @ Sun, 21 Jun 2020 21:52:17: start X-correlation... INFO @ Sun, 21 Jun 2020 21:52:17: end of X-cor INFO @ Sun, 21 Jun 2020 21:52:17: #2 finished! INFO @ Sun, 21 Jun 2020 21:52:17: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 21:52:17: #2 alternative fragment length(s) may be 4,60 bps INFO @ Sun, 21 Jun 2020 21:52:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX511134/SRX511134.20_model.r WARNING @ Sun, 21 Jun 2020 21:52:17: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:52:17: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Sun, 21 Jun 2020 21:52:17: #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 21:52:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:52:17: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:52:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:52:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX511134/SRX511134.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:52:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX511134/SRX511134.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:52:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX511134/SRX511134.20_summits.bed INFO @ Sun, 21 Jun 2020 21:52:38: Done! pass1 - making usageList (220 chroms): 1 millis pass2 - checking and writing primary data (450 records, 4 fields): 34 millis CompletedMACS2peakCalling