Job ID = 6627183 SRX = SRX8521310 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:28:04 prefetch.2.10.7: 1) Downloading 'SRR11978689'... 2020-07-14T01:28:04 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:29:47 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:29:47 prefetch.2.10.7: 'SRR11978689' is valid 2020-07-14T01:29:47 prefetch.2.10.7: 1) 'SRR11978689' was downloaded successfully 2020-07-14T01:29:47 prefetch.2.10.7: 'SRR11978689' has 0 unresolved dependencies Read 11875032 spots for SRR11978689/SRR11978689.sra Written 11875032 spots for SRR11978689/SRR11978689.sra 2020-07-14T01:30:40 prefetch.2.10.7: 1) Downloading 'SRR11978690'... 2020-07-14T01:30:40 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:31:52 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:31:52 prefetch.2.10.7: 'SRR11978690' is valid 2020-07-14T01:31:52 prefetch.2.10.7: 1) 'SRR11978690' was downloaded successfully 2020-07-14T01:31:52 prefetch.2.10.7: 'SRR11978690' has 0 unresolved dependencies Read 11926429 spots for SRR11978690/SRR11978690.sra Written 11926429 spots for SRR11978690/SRR11978690.sra 2020-07-14T01:32:46 prefetch.2.10.7: 1) Downloading 'SRR11978691'... 2020-07-14T01:32:46 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:34:12 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:34:13 prefetch.2.10.7: 'SRR11978691' is valid 2020-07-14T01:34:13 prefetch.2.10.7: 1) 'SRR11978691' was downloaded successfully 2020-07-14T01:34:13 prefetch.2.10.7: 'SRR11978691' has 0 unresolved dependencies Read 11960257 spots for SRR11978691/SRR11978691.sra Written 11960257 spots for SRR11978691/SRR11978691.sra 2020-07-14T01:35:06 prefetch.2.10.7: 1) Downloading 'SRR11978692'... 2020-07-14T01:35:06 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:36:40 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:36:40 prefetch.2.10.7: 'SRR11978692' is valid 2020-07-14T01:36:40 prefetch.2.10.7: 1) 'SRR11978692' was downloaded successfully 2020-07-14T01:36:40 prefetch.2.10.7: 'SRR11978692' has 0 unresolved dependencies Read 12078729 spots for SRR11978692/SRR11978692.sra Written 12078729 spots for SRR11978692/SRR11978692.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627430 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:31 47840447 reads; of these: 47840447 (100.00%) were unpaired; of these: 43139271 (90.17%) aligned 0 times 3583272 (7.49%) aligned exactly 1 time 1117904 (2.34%) aligned >1 times 9.83% overall alignment rate Time searching: 00:06:31 Overall time: 00:06:31 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 872823 / 4701176 = 0.1857 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, 14 Jul 2020 10:45:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521310/SRX8521310.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521310/SRX8521310.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521310/SRX8521310.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521310/SRX8521310.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 @ Tue, 14 Jul 2020 10:45:52: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:45:52: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:45:58: 1000000 INFO @ Tue, 14 Jul 2020 10:46:03: 2000000 INFO @ Tue, 14 Jul 2020 10:46:08: 3000000 INFO @ Tue, 14 Jul 2020 10:46:13: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 10:46:13: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 10:46:13: #1 total tags in treatment: 3828353 INFO @ Tue, 14 Jul 2020 10:46:13: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:46:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:46:13: #1 tags after filtering in treatment: 3828353 INFO @ Tue, 14 Jul 2020 10:46:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:46:13: #1 finished! INFO @ Tue, 14 Jul 2020 10:46:13: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:46:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:46:13: #2 number of paired peaks: 630 WARNING @ Tue, 14 Jul 2020 10:46:13: Fewer paired peaks (630) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 630 pairs to build model! INFO @ Tue, 14 Jul 2020 10:46:13: start model_add_line... INFO @ Tue, 14 Jul 2020 10:46:13: start X-correlation... INFO @ Tue, 14 Jul 2020 10:46:13: end of X-cor INFO @ Tue, 14 Jul 2020 10:46:13: #2 finished! INFO @ Tue, 14 Jul 2020 10:46:13: #2 predicted fragment length is 63 bps INFO @ Tue, 14 Jul 2020 10:46:13: #2 alternative fragment length(s) may be 63 bps INFO @ Tue, 14 Jul 2020 10:46:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521310/SRX8521310.05_model.r WARNING @ Tue, 14 Jul 2020 10:46:13: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:46:13: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Tue, 14 Jul 2020 10:46:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:46:13: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:46:13: #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, 14 Jul 2020 10:46:22: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:46:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521310/SRX8521310.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521310/SRX8521310.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521310/SRX8521310.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521310/SRX8521310.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 @ Tue, 14 Jul 2020 10:46:22: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:46:22: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:46:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521310/SRX8521310.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:46:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521310/SRX8521310.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:46:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521310/SRX8521310.05_summits.bed INFO @ Tue, 14 Jul 2020 10:46:26: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1771 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:46:28: 1000000 INFO @ Tue, 14 Jul 2020 10:46:34: 2000000 INFO @ Tue, 14 Jul 2020 10:46:40: 3000000 INFO @ Tue, 14 Jul 2020 10:46:45: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 10:46:45: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 10:46:45: #1 total tags in treatment: 3828353 INFO @ Tue, 14 Jul 2020 10:46:45: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:46:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:46:45: #1 tags after filtering in treatment: 3828353 INFO @ Tue, 14 Jul 2020 10:46:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:46:45: #1 finished! INFO @ Tue, 14 Jul 2020 10:46:45: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:46:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:46:45: #2 number of paired peaks: 630 WARNING @ Tue, 14 Jul 2020 10:46:45: Fewer paired peaks (630) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 630 pairs to build model! INFO @ Tue, 14 Jul 2020 10:46:45: start model_add_line... INFO @ Tue, 14 Jul 2020 10:46:45: start X-correlation... INFO @ Tue, 14 Jul 2020 10:46:45: end of X-cor INFO @ Tue, 14 Jul 2020 10:46:45: #2 finished! INFO @ Tue, 14 Jul 2020 10:46:45: #2 predicted fragment length is 63 bps INFO @ Tue, 14 Jul 2020 10:46:45: #2 alternative fragment length(s) may be 63 bps INFO @ Tue, 14 Jul 2020 10:46:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521310/SRX8521310.10_model.r WARNING @ Tue, 14 Jul 2020 10:46:45: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:46:45: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Tue, 14 Jul 2020 10:46:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:46:45: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:46:45: #3 Pre-compute pvalue-qvalue table... 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, 14 Jul 2020 10:46:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521310/SRX8521310.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521310/SRX8521310.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521310/SRX8521310.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521310/SRX8521310.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 @ Tue, 14 Jul 2020 10:46:52: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:46:52: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:46:54: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:46:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521310/SRX8521310.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:46:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521310/SRX8521310.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:46:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521310/SRX8521310.10_summits.bed INFO @ Tue, 14 Jul 2020 10:46:57: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (801 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:46:58: 1000000 INFO @ Tue, 14 Jul 2020 10:47:04: 2000000 INFO @ Tue, 14 Jul 2020 10:47:10: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:47:15: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 10:47:15: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 10:47:15: #1 total tags in treatment: 3828353 INFO @ Tue, 14 Jul 2020 10:47:15: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:47:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:47:15: #1 tags after filtering in treatment: 3828353 INFO @ Tue, 14 Jul 2020 10:47:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:47:15: #1 finished! INFO @ Tue, 14 Jul 2020 10:47:15: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:47:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:47:16: #2 number of paired peaks: 630 WARNING @ Tue, 14 Jul 2020 10:47:16: Fewer paired peaks (630) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 630 pairs to build model! INFO @ Tue, 14 Jul 2020 10:47:16: start model_add_line... INFO @ Tue, 14 Jul 2020 10:47:16: start X-correlation... INFO @ Tue, 14 Jul 2020 10:47:16: end of X-cor INFO @ Tue, 14 Jul 2020 10:47:16: #2 finished! INFO @ Tue, 14 Jul 2020 10:47:16: #2 predicted fragment length is 63 bps INFO @ Tue, 14 Jul 2020 10:47:16: #2 alternative fragment length(s) may be 63 bps INFO @ Tue, 14 Jul 2020 10:47:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521310/SRX8521310.20_model.r WARNING @ Tue, 14 Jul 2020 10:47:16: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:47:16: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Tue, 14 Jul 2020 10:47:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:47:16: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:47:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:47:24: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:47:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521310/SRX8521310.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:47:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521310/SRX8521310.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:47:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521310/SRX8521310.20_summits.bed INFO @ Tue, 14 Jul 2020 10:47:28: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (186 records, 4 fields): 2 millis CompletedMACS2peakCalling