Job ID = 6627110 SRX = SRX8521288 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T00:56:06 prefetch.2.10.7: 1) Downloading 'SRR11978442'... 2020-07-14T00:56:06 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T00:57:17 prefetch.2.10.7: HTTPS download succeed 2020-07-14T00:57:18 prefetch.2.10.7: 'SRR11978442' is valid 2020-07-14T00:57:18 prefetch.2.10.7: 1) 'SRR11978442' was downloaded successfully 2020-07-14T00:57:18 prefetch.2.10.7: 'SRR11978442' has 0 unresolved dependencies Read 14517418 spots for SRR11978442/SRR11978442.sra Written 14517418 spots for SRR11978442/SRR11978442.sra 2020-07-14T00:58:21 prefetch.2.10.7: 1) Downloading 'SRR11978443'... 2020-07-14T00:58:21 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:00:00 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:00:00 prefetch.2.10.7: 'SRR11978443' is valid 2020-07-14T01:00:00 prefetch.2.10.7: 1) 'SRR11978443' was downloaded successfully 2020-07-14T01:00:00 prefetch.2.10.7: 'SRR11978443' has 0 unresolved dependencies Read 14366530 spots for SRR11978443/SRR11978443.sra Written 14366530 spots for SRR11978443/SRR11978443.sra 2020-07-14T01:00:58 prefetch.2.10.7: 1) Downloading 'SRR11978444'... 2020-07-14T01:00:58 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:05:52 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:05:52 prefetch.2.10.7: 'SRR11978444' is valid 2020-07-14T01:05:52 prefetch.2.10.7: 1) 'SRR11978444' was downloaded successfully 2020-07-14T01:05:52 prefetch.2.10.7: 'SRR11978444' has 0 unresolved dependencies Read 14811991 spots for SRR11978444/SRR11978444.sra Written 14811991 spots for SRR11978444/SRR11978444.sra 2020-07-14T01:06:55 prefetch.2.10.7: 1) Downloading 'SRR11978445'... 2020-07-14T01:06:55 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:08:27 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:08:27 prefetch.2.10.7: 'SRR11978445' is valid 2020-07-14T01:08:27 prefetch.2.10.7: 1) 'SRR11978445' was downloaded successfully 2020-07-14T01:08:27 prefetch.2.10.7: 'SRR11978445' has 0 unresolved dependencies Read 14690455 spots for SRR11978445/SRR11978445.sra Written 14690455 spots for SRR11978445/SRR11978445.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627352 ("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: 00:07:51 58386394 reads; of these: 58386394 (100.00%) were unpaired; of these: 50253298 (86.07%) aligned 0 times 6287797 (10.77%) aligned exactly 1 time 1845299 (3.16%) aligned >1 times 13.93% overall alignment rate Time searching: 00:07:51 Overall time: 00:07:51 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] 2249928 / 8133096 = 0.2766 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 10:20:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521288/SRX8521288.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521288/SRX8521288.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521288/SRX8521288.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521288/SRX8521288.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 10:20:07: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:20:07: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:20:13: 1000000 INFO @ Tue, 14 Jul 2020 10:20:19: 2000000 INFO @ Tue, 14 Jul 2020 10:20:25: 3000000 INFO @ Tue, 14 Jul 2020 10:20:31: 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 @ Tue, 14 Jul 2020 10:20:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521288/SRX8521288.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521288/SRX8521288.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521288/SRX8521288.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521288/SRX8521288.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 10:20:37: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:20:37: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:20:38: 5000000 INFO @ Tue, 14 Jul 2020 10:20:44: #1 tag size is determined as 67 bps INFO @ Tue, 14 Jul 2020 10:20:44: #1 tag size = 67 INFO @ Tue, 14 Jul 2020 10:20:44: #1 total tags in treatment: 5883168 INFO @ Tue, 14 Jul 2020 10:20:44: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:20:44: #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 10:20:44: #1 tags after filtering in treatment: 5883168 INFO @ Tue, 14 Jul 2020 10:20:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:20:44: #1 finished! INFO @ Tue, 14 Jul 2020 10:20:44: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:20:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:20:45: #2 number of paired peaks: 535 WARNING @ Tue, 14 Jul 2020 10:20:45: Fewer paired peaks (535) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 535 pairs to build model! INFO @ Tue, 14 Jul 2020 10:20:45: start model_add_line... INFO @ Tue, 14 Jul 2020 10:20:45: start X-correlation... INFO @ Tue, 14 Jul 2020 10:20:45: end of X-cor INFO @ Tue, 14 Jul 2020 10:20:45: #2 finished! INFO @ Tue, 14 Jul 2020 10:20:45: #2 predicted fragment length is 60 bps INFO @ Tue, 14 Jul 2020 10:20:45: #2 alternative fragment length(s) may be 60 bps INFO @ Tue, 14 Jul 2020 10:20:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521288/SRX8521288.05_model.r WARNING @ Tue, 14 Jul 2020 10:20:45: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:20:45: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Tue, 14 Jul 2020 10:20:45: #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 10:20:45: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:20:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:20:45: 1000000 INFO @ Tue, 14 Jul 2020 10:20:53: 2000000 INFO @ Tue, 14 Jul 2020 10:20:56: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:21:00: 3000000 INFO @ Tue, 14 Jul 2020 10:21:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521288/SRX8521288.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:21:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521288/SRX8521288.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:21:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521288/SRX8521288.05_summits.bed INFO @ Tue, 14 Jul 2020 10:21:02: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2806 records, 4 fields): 4 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, 14 Jul 2020 10:21:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521288/SRX8521288.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521288/SRX8521288.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521288/SRX8521288.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521288/SRX8521288.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 10:21:07: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:21:07: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:21:08: 4000000 INFO @ Tue, 14 Jul 2020 10:21:15: 1000000 INFO @ Tue, 14 Jul 2020 10:21:16: 5000000 INFO @ Tue, 14 Jul 2020 10:21:22: 2000000 INFO @ Tue, 14 Jul 2020 10:21:23: #1 tag size is determined as 67 bps INFO @ Tue, 14 Jul 2020 10:21:23: #1 tag size = 67 INFO @ Tue, 14 Jul 2020 10:21:23: #1 total tags in treatment: 5883168 INFO @ Tue, 14 Jul 2020 10:21:23: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:21:23: #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 10:21:23: #1 tags after filtering in treatment: 5883168 INFO @ Tue, 14 Jul 2020 10:21:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:21:23: #1 finished! INFO @ Tue, 14 Jul 2020 10:21:23: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:21:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:21:23: #2 number of paired peaks: 535 WARNING @ Tue, 14 Jul 2020 10:21:23: Fewer paired peaks (535) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 535 pairs to build model! INFO @ Tue, 14 Jul 2020 10:21:23: start model_add_line... INFO @ Tue, 14 Jul 2020 10:21:23: start X-correlation... INFO @ Tue, 14 Jul 2020 10:21:23: end of X-cor INFO @ Tue, 14 Jul 2020 10:21:23: #2 finished! INFO @ Tue, 14 Jul 2020 10:21:23: #2 predicted fragment length is 60 bps INFO @ Tue, 14 Jul 2020 10:21:23: #2 alternative fragment length(s) may be 60 bps INFO @ Tue, 14 Jul 2020 10:21:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521288/SRX8521288.10_model.r WARNING @ Tue, 14 Jul 2020 10:21:23: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:21:23: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Tue, 14 Jul 2020 10:21:23: #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 10:21:23: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:21:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:21:29: 3000000 INFO @ Tue, 14 Jul 2020 10:21:35: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:21:36: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:21:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521288/SRX8521288.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:21:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521288/SRX8521288.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:21:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521288/SRX8521288.10_summits.bed INFO @ Tue, 14 Jul 2020 10:21:41: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (936 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:21:42: 5000000 INFO @ Tue, 14 Jul 2020 10:21:48: #1 tag size is determined as 67 bps INFO @ Tue, 14 Jul 2020 10:21:48: #1 tag size = 67 INFO @ Tue, 14 Jul 2020 10:21:48: #1 total tags in treatment: 5883168 INFO @ Tue, 14 Jul 2020 10:21:48: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:21:48: #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 10:21:48: #1 tags after filtering in treatment: 5883168 INFO @ Tue, 14 Jul 2020 10:21:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:21:48: #1 finished! INFO @ Tue, 14 Jul 2020 10:21:48: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:21:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:21:49: #2 number of paired peaks: 535 WARNING @ Tue, 14 Jul 2020 10:21:49: Fewer paired peaks (535) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 535 pairs to build model! INFO @ Tue, 14 Jul 2020 10:21:49: start model_add_line... INFO @ Tue, 14 Jul 2020 10:21:49: start X-correlation... INFO @ Tue, 14 Jul 2020 10:21:49: end of X-cor INFO @ Tue, 14 Jul 2020 10:21:49: #2 finished! INFO @ Tue, 14 Jul 2020 10:21:49: #2 predicted fragment length is 60 bps INFO @ Tue, 14 Jul 2020 10:21:49: #2 alternative fragment length(s) may be 60 bps INFO @ Tue, 14 Jul 2020 10:21:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521288/SRX8521288.20_model.r WARNING @ Tue, 14 Jul 2020 10:21:49: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:21:49: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Tue, 14 Jul 2020 10:21:49: #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 10:21:49: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:21:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:22:01: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:22:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521288/SRX8521288.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:22:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521288/SRX8521288.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:22:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521288/SRX8521288.20_summits.bed INFO @ Tue, 14 Jul 2020 10:22:07: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (231 records, 4 fields): 2 millis CompletedMACS2peakCalling