Job ID = 6627322 SRX = SRX8521370 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:58:59 prefetch.2.10.7: 1) Downloading 'SRR11978146'... 2020-07-14T01:58:59 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:10:32 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:10:32 prefetch.2.10.7: 'SRR11978146' is valid 2020-07-14T02:10:32 prefetch.2.10.7: 1) 'SRR11978146' was downloaded successfully 2020-07-14T02:10:32 prefetch.2.10.7: 'SRR11978146' has 0 unresolved dependencies Read 9653420 spots for SRR11978146/SRR11978146.sra Written 9653420 spots for SRR11978146/SRR11978146.sra 2020-07-14T02:11:21 prefetch.2.10.7: 1) Downloading 'SRR11978147'... 2020-07-14T02:11:21 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:12:29 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:12:30 prefetch.2.10.7: 'SRR11978147' is valid 2020-07-14T02:12:30 prefetch.2.10.7: 1) 'SRR11978147' was downloaded successfully 2020-07-14T02:12:30 prefetch.2.10.7: 'SRR11978147' has 0 unresolved dependencies Read 8892823 spots for SRR11978147/SRR11978147.sra Written 8892823 spots for SRR11978147/SRR11978147.sra 2020-07-14T02:13:16 prefetch.2.10.7: 1) Downloading 'SRR11978148'... 2020-07-14T02:13:16 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:14:32 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:14:33 prefetch.2.10.7: 'SRR11978148' is valid 2020-07-14T02:14:33 prefetch.2.10.7: 1) 'SRR11978148' was downloaded successfully 2020-07-14T02:14:33 prefetch.2.10.7: 'SRR11978148' has 0 unresolved dependencies Read 9283853 spots for SRR11978148/SRR11978148.sra Written 9283853 spots for SRR11978148/SRR11978148.sra 2020-07-14T02:15:18 prefetch.2.10.7: 1) Downloading 'SRR11978149'... 2020-07-14T02:15:18 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:16:21 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:16:21 prefetch.2.10.7: 'SRR11978149' is valid 2020-07-14T02:16:21 prefetch.2.10.7: 1) 'SRR11978149' was downloaded successfully 2020-07-14T02:16:22 prefetch.2.10.7: 'SRR11978149' has 0 unresolved dependencies Read 9310624 spots for SRR11978149/SRR11978149.sra Written 9310624 spots for SRR11978149/SRR11978149.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627567 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:24 37140720 reads; of these: 37140720 (100.00%) were unpaired; of these: 31877214 (85.83%) aligned 0 times 3897590 (10.49%) aligned exactly 1 time 1365916 (3.68%) aligned >1 times 14.17% overall alignment rate Time searching: 00:05:25 Overall time: 00:05:25 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] 910224 / 5263506 = 0.1729 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 11:24:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521370/SRX8521370.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521370/SRX8521370.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521370/SRX8521370.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521370/SRX8521370.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 11:24:37: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:24:37: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:24:43: 1000000 INFO @ Tue, 14 Jul 2020 11:24:49: 2000000 INFO @ Tue, 14 Jul 2020 11:24:55: 3000000 INFO @ Tue, 14 Jul 2020 11:25:01: 4000000 INFO @ Tue, 14 Jul 2020 11:25:03: #1 tag size is determined as 56 bps INFO @ Tue, 14 Jul 2020 11:25:03: #1 tag size = 56 INFO @ Tue, 14 Jul 2020 11:25:03: #1 total tags in treatment: 4353282 INFO @ Tue, 14 Jul 2020 11:25:03: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:25:03: #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 11:25:03: #1 tags after filtering in treatment: 4353282 INFO @ Tue, 14 Jul 2020 11:25:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:25:03: #1 finished! INFO @ Tue, 14 Jul 2020 11:25:03: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:25:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:25:03: #2 number of paired peaks: 467 WARNING @ Tue, 14 Jul 2020 11:25:03: Fewer paired peaks (467) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 467 pairs to build model! INFO @ Tue, 14 Jul 2020 11:25:03: start model_add_line... INFO @ Tue, 14 Jul 2020 11:25:03: start X-correlation... INFO @ Tue, 14 Jul 2020 11:25:03: end of X-cor INFO @ Tue, 14 Jul 2020 11:25:03: #2 finished! INFO @ Tue, 14 Jul 2020 11:25:03: #2 predicted fragment length is 59 bps INFO @ Tue, 14 Jul 2020 11:25:03: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 14 Jul 2020 11:25:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521370/SRX8521370.05_model.r WARNING @ Tue, 14 Jul 2020 11:25:03: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:25:03: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 14 Jul 2020 11:25:03: #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 11:25:03: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:25:03: #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 11:25:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521370/SRX8521370.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521370/SRX8521370.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521370/SRX8521370.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521370/SRX8521370.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 11:25:07: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:25:07: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:25:13: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:25:13: 1000000 INFO @ Tue, 14 Jul 2020 11:25:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521370/SRX8521370.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:25:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521370/SRX8521370.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:25:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521370/SRX8521370.05_summits.bed INFO @ Tue, 14 Jul 2020 11:25:18: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1629 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:25:19: 2000000 INFO @ Tue, 14 Jul 2020 11:25:25: 3000000 INFO @ Tue, 14 Jul 2020 11:25:31: 4000000 INFO @ Tue, 14 Jul 2020 11:25:33: #1 tag size is determined as 56 bps INFO @ Tue, 14 Jul 2020 11:25:33: #1 tag size = 56 INFO @ Tue, 14 Jul 2020 11:25:33: #1 total tags in treatment: 4353282 INFO @ Tue, 14 Jul 2020 11:25:33: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:25:33: #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 11:25:33: #1 tags after filtering in treatment: 4353282 INFO @ Tue, 14 Jul 2020 11:25:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:25:33: #1 finished! INFO @ Tue, 14 Jul 2020 11:25:33: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:25:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:25:33: #2 number of paired peaks: 467 WARNING @ Tue, 14 Jul 2020 11:25:33: Fewer paired peaks (467) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 467 pairs to build model! INFO @ Tue, 14 Jul 2020 11:25:33: start model_add_line... INFO @ Tue, 14 Jul 2020 11:25:33: start X-correlation... INFO @ Tue, 14 Jul 2020 11:25:33: end of X-cor INFO @ Tue, 14 Jul 2020 11:25:33: #2 finished! INFO @ Tue, 14 Jul 2020 11:25:33: #2 predicted fragment length is 59 bps INFO @ Tue, 14 Jul 2020 11:25:33: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 14 Jul 2020 11:25:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521370/SRX8521370.10_model.r WARNING @ Tue, 14 Jul 2020 11:25:33: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:25:33: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 14 Jul 2020 11:25:33: #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 11:25:33: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:25:33: #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 11:25:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521370/SRX8521370.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521370/SRX8521370.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521370/SRX8521370.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521370/SRX8521370.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 11:25:37: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:25:37: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:25:42: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:25:43: 1000000 INFO @ Tue, 14 Jul 2020 11:25:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521370/SRX8521370.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:25:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521370/SRX8521370.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:25:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521370/SRX8521370.10_summits.bed INFO @ Tue, 14 Jul 2020 11:25:47: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (582 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:25:49: 2000000 INFO @ Tue, 14 Jul 2020 11:25:55: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:26:01: 4000000 INFO @ Tue, 14 Jul 2020 11:26:03: #1 tag size is determined as 56 bps INFO @ Tue, 14 Jul 2020 11:26:03: #1 tag size = 56 INFO @ Tue, 14 Jul 2020 11:26:03: #1 total tags in treatment: 4353282 INFO @ Tue, 14 Jul 2020 11:26:03: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:26:03: #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 11:26:03: #1 tags after filtering in treatment: 4353282 INFO @ Tue, 14 Jul 2020 11:26:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:26:03: #1 finished! INFO @ Tue, 14 Jul 2020 11:26:03: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:26:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:26:03: #2 number of paired peaks: 467 WARNING @ Tue, 14 Jul 2020 11:26:03: Fewer paired peaks (467) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 467 pairs to build model! INFO @ Tue, 14 Jul 2020 11:26:03: start model_add_line... INFO @ Tue, 14 Jul 2020 11:26:03: start X-correlation... INFO @ Tue, 14 Jul 2020 11:26:03: end of X-cor INFO @ Tue, 14 Jul 2020 11:26:03: #2 finished! INFO @ Tue, 14 Jul 2020 11:26:03: #2 predicted fragment length is 59 bps INFO @ Tue, 14 Jul 2020 11:26:03: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 14 Jul 2020 11:26:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521370/SRX8521370.20_model.r WARNING @ Tue, 14 Jul 2020 11:26:03: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:26:03: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 14 Jul 2020 11:26:03: #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 11:26:03: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:26:03: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:26:13: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:26:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521370/SRX8521370.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:26:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521370/SRX8521370.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:26:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521370/SRX8521370.20_summits.bed INFO @ Tue, 14 Jul 2020 11:26:17: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (127 records, 4 fields): 2 millis CompletedMACS2peakCalling