Job ID = 6627443 SRX = SRX8521383 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T02:29:02 prefetch.2.10.7: 1) Downloading 'SRR11978274'... 2020-07-14T02:29:02 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:30:12 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:30:12 prefetch.2.10.7: 'SRR11978274' is valid 2020-07-14T02:30:12 prefetch.2.10.7: 1) 'SRR11978274' was downloaded successfully 2020-07-14T02:30:12 prefetch.2.10.7: 'SRR11978274' has 0 unresolved dependencies Read 11047028 spots for SRR11978274/SRR11978274.sra Written 11047028 spots for SRR11978274/SRR11978274.sra 2020-07-14T02:31:02 prefetch.2.10.7: 1) Downloading 'SRR11978275'... 2020-07-14T02:31:02 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:32:06 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:32:06 prefetch.2.10.7: 'SRR11978275' is valid 2020-07-14T02:32:06 prefetch.2.10.7: 1) 'SRR11978275' was downloaded successfully 2020-07-14T02:32:06 prefetch.2.10.7: 'SRR11978275' has 0 unresolved dependencies Read 10900368 spots for SRR11978275/SRR11978275.sra Written 10900368 spots for SRR11978275/SRR11978275.sra 2020-07-14T02:32:52 prefetch.2.10.7: 1) Downloading 'SRR11978276'... 2020-07-14T02:32:52 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:33:58 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:33:59 prefetch.2.10.7: 'SRR11978276' is valid 2020-07-14T02:33:59 prefetch.2.10.7: 1) 'SRR11978276' was downloaded successfully 2020-07-14T02:33:59 prefetch.2.10.7: 'SRR11978276' has 0 unresolved dependencies Read 10872114 spots for SRR11978276/SRR11978276.sra Written 10872114 spots for SRR11978276/SRR11978276.sra 2020-07-14T02:34:49 prefetch.2.10.7: 1) Downloading 'SRR11978277'... 2020-07-14T02:34:49 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:36:02 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:36:03 prefetch.2.10.7: 'SRR11978277' is valid 2020-07-14T02:36:03 prefetch.2.10.7: 1) 'SRR11978277' was downloaded successfully 2020-07-14T02:36:03 prefetch.2.10.7: 'SRR11978277' has 0 unresolved dependencies Read 10941931 spots for SRR11978277/SRR11978277.sra Written 10941931 spots for SRR11978277/SRR11978277.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627616 ("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: 00:05:51 43761441 reads; of these: 43761441 (100.00%) were unpaired; of these: 40063376 (91.55%) aligned 0 times 2730290 (6.24%) aligned exactly 1 time 967775 (2.21%) aligned >1 times 8.45% overall alignment rate Time searching: 00:05:51 Overall time: 00:05:51 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] 730354 / 3698065 = 0.1975 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 11:44:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521383/SRX8521383.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521383/SRX8521383.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521383/SRX8521383.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521383/SRX8521383.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 11:44:15: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:44:15: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:44:22: 1000000 INFO @ Tue, 14 Jul 2020 11:44:29: 2000000 INFO @ Tue, 14 Jul 2020 11:44:36: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 11:44:36: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 11:44:36: #1 total tags in treatment: 2967711 INFO @ Tue, 14 Jul 2020 11:44:36: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:44:36: #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 11:44:36: #1 tags after filtering in treatment: 2967711 INFO @ Tue, 14 Jul 2020 11:44:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:44:36: #1 finished! INFO @ Tue, 14 Jul 2020 11:44:36: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:44:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:44:36: #2 number of paired peaks: 786 WARNING @ Tue, 14 Jul 2020 11:44:36: Fewer paired peaks (786) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 786 pairs to build model! INFO @ Tue, 14 Jul 2020 11:44:36: start model_add_line... INFO @ Tue, 14 Jul 2020 11:44:36: start X-correlation... INFO @ Tue, 14 Jul 2020 11:44:36: end of X-cor INFO @ Tue, 14 Jul 2020 11:44:36: #2 finished! INFO @ Tue, 14 Jul 2020 11:44:36: #2 predicted fragment length is 60 bps INFO @ Tue, 14 Jul 2020 11:44:36: #2 alternative fragment length(s) may be 60,527 bps INFO @ Tue, 14 Jul 2020 11:44:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521383/SRX8521383.05_model.r WARNING @ Tue, 14 Jul 2020 11:44:36: #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 11:44:36: #2 You may need to consider one of the other alternative d(s): 60,527 WARNING @ Tue, 14 Jul 2020 11:44:36: #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 11:44:36: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:44:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:44:43: #3 Call peaks for each chromosome... 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 11:44:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521383/SRX8521383.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521383/SRX8521383.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521383/SRX8521383.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521383/SRX8521383.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 11:44:45: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:44:45: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:44:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521383/SRX8521383.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:44:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521383/SRX8521383.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:44:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521383/SRX8521383.05_summits.bed INFO @ Tue, 14 Jul 2020 11:44:46: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1466 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:44:51: 1000000 INFO @ Tue, 14 Jul 2020 11:44:57: 2000000 INFO @ Tue, 14 Jul 2020 11:45:03: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 11:45:03: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 11:45:03: #1 total tags in treatment: 2967711 INFO @ Tue, 14 Jul 2020 11:45:03: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:45:03: #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 11:45:03: #1 tags after filtering in treatment: 2967711 INFO @ Tue, 14 Jul 2020 11:45:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:45:03: #1 finished! INFO @ Tue, 14 Jul 2020 11:45:03: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:45:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:45:03: #2 number of paired peaks: 786 WARNING @ Tue, 14 Jul 2020 11:45:03: Fewer paired peaks (786) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 786 pairs to build model! INFO @ Tue, 14 Jul 2020 11:45:03: start model_add_line... INFO @ Tue, 14 Jul 2020 11:45:03: start X-correlation... INFO @ Tue, 14 Jul 2020 11:45:03: end of X-cor INFO @ Tue, 14 Jul 2020 11:45:03: #2 finished! INFO @ Tue, 14 Jul 2020 11:45:03: #2 predicted fragment length is 60 bps INFO @ Tue, 14 Jul 2020 11:45:03: #2 alternative fragment length(s) may be 60,527 bps INFO @ Tue, 14 Jul 2020 11:45:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521383/SRX8521383.10_model.r WARNING @ Tue, 14 Jul 2020 11:45:03: #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 11:45:03: #2 You may need to consider one of the other alternative d(s): 60,527 WARNING @ Tue, 14 Jul 2020 11:45:03: #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 11:45:03: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:45:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:45:09: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:45:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521383/SRX8521383.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:45:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521383/SRX8521383.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:45:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521383/SRX8521383.10_summits.bed INFO @ Tue, 14 Jul 2020 11:45:13: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (624 records, 4 fields): 2 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 11:45:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521383/SRX8521383.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521383/SRX8521383.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521383/SRX8521383.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521383/SRX8521383.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 11:45:15: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:45:15: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:45:21: 1000000 INFO @ Tue, 14 Jul 2020 11:45:27: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:45:33: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 11:45:33: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 11:45:33: #1 total tags in treatment: 2967711 INFO @ Tue, 14 Jul 2020 11:45:33: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:45:33: #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 11:45:33: #1 tags after filtering in treatment: 2967711 INFO @ Tue, 14 Jul 2020 11:45:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:45:33: #1 finished! INFO @ Tue, 14 Jul 2020 11:45:33: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:45:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:45:34: #2 number of paired peaks: 786 WARNING @ Tue, 14 Jul 2020 11:45:34: Fewer paired peaks (786) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 786 pairs to build model! INFO @ Tue, 14 Jul 2020 11:45:34: start model_add_line... INFO @ Tue, 14 Jul 2020 11:45:34: start X-correlation... INFO @ Tue, 14 Jul 2020 11:45:34: end of X-cor INFO @ Tue, 14 Jul 2020 11:45:34: #2 finished! INFO @ Tue, 14 Jul 2020 11:45:34: #2 predicted fragment length is 60 bps INFO @ Tue, 14 Jul 2020 11:45:34: #2 alternative fragment length(s) may be 60,527 bps INFO @ Tue, 14 Jul 2020 11:45:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521383/SRX8521383.20_model.r WARNING @ Tue, 14 Jul 2020 11:45:34: #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 11:45:34: #2 You may need to consider one of the other alternative d(s): 60,527 WARNING @ Tue, 14 Jul 2020 11:45:34: #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 11:45:34: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:45:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:45:40: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:45:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521383/SRX8521383.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:45:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521383/SRX8521383.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:45:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521383/SRX8521383.20_summits.bed INFO @ Tue, 14 Jul 2020 11:45:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (139 records, 4 fields): 1 millis CompletedMACS2peakCalling