Job ID = 6627176 SRX = SRX8521307 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:26:46 prefetch.2.10.7: 1) Downloading 'SRR11978677'... 2020-07-14T01:26:46 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:28:03 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:28:04 prefetch.2.10.7: 'SRR11978677' is valid 2020-07-14T01:28:04 prefetch.2.10.7: 1) 'SRR11978677' was downloaded successfully 2020-07-14T01:28:04 prefetch.2.10.7: 'SRR11978677' has 0 unresolved dependencies Read 11434610 spots for SRR11978677/SRR11978677.sra Written 11434610 spots for SRR11978677/SRR11978677.sra 2020-07-14T01:32:56 prefetch.2.10.7: 1) Downloading 'SRR11978678'... 2020-07-14T01:32:56 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:34:16 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:34:16 prefetch.2.10.7: 'SRR11978678' is valid 2020-07-14T01:34:16 prefetch.2.10.7: 1) 'SRR11978678' was downloaded successfully 2020-07-14T01:34:16 prefetch.2.10.7: 'SRR11978678' has 0 unresolved dependencies Read 11375553 spots for SRR11978678/SRR11978678.sra Written 11375553 spots for SRR11978678/SRR11978678.sra 2020-07-14T01:35:09 prefetch.2.10.7: 1) Downloading 'SRR11978679'... 2020-07-14T01:35:09 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:36:57 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:36:58 prefetch.2.10.7: 'SRR11978679' is valid 2020-07-14T01:36:58 prefetch.2.10.7: 1) 'SRR11978679' was downloaded successfully 2020-07-14T01:36:58 prefetch.2.10.7: 'SRR11978679' has 0 unresolved dependencies Read 11171852 spots for SRR11978679/SRR11978679.sra Written 11171852 spots for SRR11978679/SRR11978679.sra 2020-07-14T01:37:51 prefetch.2.10.7: 1) Downloading 'SRR11978680'... 2020-07-14T01:37:51 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:39:12 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:39:13 prefetch.2.10.7: 'SRR11978680' is valid 2020-07-14T01:39:13 prefetch.2.10.7: 1) 'SRR11978680' was downloaded successfully 2020-07-14T01:39:13 prefetch.2.10.7: 'SRR11978680' has 0 unresolved dependencies Read 11331688 spots for SRR11978680/SRR11978680.sra Written 11331688 spots for SRR11978680/SRR11978680.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627440 ("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: 00:06:54 45313703 reads; of these: 45313703 (100.00%) were unpaired; of these: 40970211 (90.41%) aligned 0 times 3319492 (7.33%) aligned exactly 1 time 1024000 (2.26%) aligned >1 times 9.59% overall alignment rate Time searching: 00:06:54 Overall time: 00:06:54 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] 787821 / 4343492 = 0.1814 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 10:48:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521307/SRX8521307.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521307/SRX8521307.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521307/SRX8521307.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521307/SRX8521307.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 10:48:43: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:48:43: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:48:51: 1000000 INFO @ Tue, 14 Jul 2020 10:48:59: 2000000 INFO @ Tue, 14 Jul 2020 10:49:06: 3000000 INFO @ Tue, 14 Jul 2020 10:49:10: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 10:49:10: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 10:49:10: #1 total tags in treatment: 3555671 INFO @ Tue, 14 Jul 2020 10:49:10: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:49:10: #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 10:49:10: #1 tags after filtering in treatment: 3555671 INFO @ Tue, 14 Jul 2020 10:49:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:49:10: #1 finished! INFO @ Tue, 14 Jul 2020 10:49:10: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:49:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:49:10: #2 number of paired peaks: 622 WARNING @ Tue, 14 Jul 2020 10:49:10: Fewer paired peaks (622) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 622 pairs to build model! INFO @ Tue, 14 Jul 2020 10:49:10: start model_add_line... INFO @ Tue, 14 Jul 2020 10:49:10: start X-correlation... INFO @ Tue, 14 Jul 2020 10:49:10: end of X-cor INFO @ Tue, 14 Jul 2020 10:49:10: #2 finished! INFO @ Tue, 14 Jul 2020 10:49:10: #2 predicted fragment length is 63 bps INFO @ Tue, 14 Jul 2020 10:49:10: #2 alternative fragment length(s) may be 63 bps INFO @ Tue, 14 Jul 2020 10:49:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521307/SRX8521307.05_model.r WARNING @ Tue, 14 Jul 2020 10:49:10: #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 10:49:10: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Tue, 14 Jul 2020 10:49:10: #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 10:49:10: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:49:10: #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 10:49:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521307/SRX8521307.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521307/SRX8521307.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521307/SRX8521307.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521307/SRX8521307.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 10:49:13: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:49:13: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:49:17: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:49:19: 1000000 INFO @ Tue, 14 Jul 2020 10:49:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521307/SRX8521307.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:49:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521307/SRX8521307.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:49:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521307/SRX8521307.05_summits.bed INFO @ Tue, 14 Jul 2020 10:49:22: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1697 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:49:26: 2000000 INFO @ Tue, 14 Jul 2020 10:49:32: 3000000 INFO @ Tue, 14 Jul 2020 10:49:36: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 10:49:36: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 10:49:36: #1 total tags in treatment: 3555671 INFO @ Tue, 14 Jul 2020 10:49:36: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:49:36: #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 10:49:36: #1 tags after filtering in treatment: 3555671 INFO @ Tue, 14 Jul 2020 10:49:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:49:36: #1 finished! INFO @ Tue, 14 Jul 2020 10:49:36: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:49:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:49:36: #2 number of paired peaks: 622 WARNING @ Tue, 14 Jul 2020 10:49:36: Fewer paired peaks (622) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 622 pairs to build model! INFO @ Tue, 14 Jul 2020 10:49:36: start model_add_line... INFO @ Tue, 14 Jul 2020 10:49:36: start X-correlation... INFO @ Tue, 14 Jul 2020 10:49:36: end of X-cor INFO @ Tue, 14 Jul 2020 10:49:36: #2 finished! INFO @ Tue, 14 Jul 2020 10:49:36: #2 predicted fragment length is 63 bps INFO @ Tue, 14 Jul 2020 10:49:36: #2 alternative fragment length(s) may be 63 bps INFO @ Tue, 14 Jul 2020 10:49:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521307/SRX8521307.10_model.r WARNING @ Tue, 14 Jul 2020 10:49:36: #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 10:49:36: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Tue, 14 Jul 2020 10:49:36: #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 10:49:36: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:49:36: #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 10:49:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521307/SRX8521307.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521307/SRX8521307.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521307/SRX8521307.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521307/SRX8521307.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 10:49:43: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:49:43: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:49:44: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:49:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521307/SRX8521307.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:49:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521307/SRX8521307.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:49:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521307/SRX8521307.10_summits.bed INFO @ Tue, 14 Jul 2020 10:49:48: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (669 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:49:51: 1000000 INFO @ Tue, 14 Jul 2020 10:49:59: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:50:07: 3000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:50:11: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 10:50:11: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 10:50:11: #1 total tags in treatment: 3555671 INFO @ Tue, 14 Jul 2020 10:50:11: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:50:11: #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 10:50:11: #1 tags after filtering in treatment: 3555671 INFO @ Tue, 14 Jul 2020 10:50:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:50:11: #1 finished! INFO @ Tue, 14 Jul 2020 10:50:11: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:50:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:50:12: #2 number of paired peaks: 622 WARNING @ Tue, 14 Jul 2020 10:50:12: Fewer paired peaks (622) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 622 pairs to build model! INFO @ Tue, 14 Jul 2020 10:50:12: start model_add_line... INFO @ Tue, 14 Jul 2020 10:50:12: start X-correlation... INFO @ Tue, 14 Jul 2020 10:50:12: end of X-cor INFO @ Tue, 14 Jul 2020 10:50:12: #2 finished! INFO @ Tue, 14 Jul 2020 10:50:12: #2 predicted fragment length is 63 bps INFO @ Tue, 14 Jul 2020 10:50:12: #2 alternative fragment length(s) may be 63 bps INFO @ Tue, 14 Jul 2020 10:50:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521307/SRX8521307.20_model.r WARNING @ Tue, 14 Jul 2020 10:50:12: #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 10:50:12: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Tue, 14 Jul 2020 10:50:12: #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 10:50:12: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:50:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:50:20: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:50:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521307/SRX8521307.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:50:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521307/SRX8521307.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:50:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521307/SRX8521307.20_summits.bed INFO @ Tue, 14 Jul 2020 10:50:24: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (130 records, 4 fields): 1 millis CompletedMACS2peakCalling