Job ID = 6627157 SRX = SRX8521300 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:22:22 prefetch.2.10.7: 1) Downloading 'SRR11978522'... 2020-07-14T01:22:22 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:24:04 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:24:05 prefetch.2.10.7: 'SRR11978522' is valid 2020-07-14T01:24:05 prefetch.2.10.7: 1) 'SRR11978522' was downloaded successfully 2020-07-14T01:24:05 prefetch.2.10.7: 'SRR11978522' has 0 unresolved dependencies Read 10188150 spots for SRR11978522/SRR11978522.sra Written 10188150 spots for SRR11978522/SRR11978522.sra 2020-07-14T01:24:54 prefetch.2.10.7: 1) Downloading 'SRR11978523'... 2020-07-14T01:24:54 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:26:30 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:26:31 prefetch.2.10.7: 'SRR11978523' is valid 2020-07-14T01:26:31 prefetch.2.10.7: 1) 'SRR11978523' was downloaded successfully 2020-07-14T01:26:31 prefetch.2.10.7: 'SRR11978523' has 0 unresolved dependencies Read 10109063 spots for SRR11978523/SRR11978523.sra Written 10109063 spots for SRR11978523/SRR11978523.sra 2020-07-14T01:27:20 prefetch.2.10.7: 1) Downloading 'SRR11978524'... 2020-07-14T01:27:20 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:29:20 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:29:20 prefetch.2.10.7: 'SRR11978524' is valid 2020-07-14T01:29:20 prefetch.2.10.7: 1) 'SRR11978524' was downloaded successfully 2020-07-14T01:29:20 prefetch.2.10.7: 'SRR11978524' has 0 unresolved dependencies Read 9744721 spots for SRR11978524/SRR11978524.sra Written 9744721 spots for SRR11978524/SRR11978524.sra 2020-07-14T01:30:07 prefetch.2.10.7: 1) Downloading 'SRR11978525'... 2020-07-14T01:30:07 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:31:45 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:31:46 prefetch.2.10.7: 'SRR11978525' is valid 2020-07-14T01:31:46 prefetch.2.10.7: 1) 'SRR11978525' was downloaded successfully 2020-07-14T01:31:46 prefetch.2.10.7: 'SRR11978525' has 0 unresolved dependencies Read 9973677 spots for SRR11978525/SRR11978525.sra Written 9973677 spots for SRR11978525/SRR11978525.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627419 ("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: 00:05:47 40015611 reads; of these: 40015611 (100.00%) were unpaired; of these: 34463587 (86.13%) aligned 0 times 4241480 (10.60%) aligned exactly 1 time 1310544 (3.28%) aligned >1 times 13.87% overall alignment rate Time searching: 00:05:47 Overall time: 00:05:47 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] 908902 / 5552024 = 0.1637 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 10:40:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521300/SRX8521300.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521300/SRX8521300.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521300/SRX8521300.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521300/SRX8521300.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 10:40:27: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:40:27: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:40:32: 1000000 INFO @ Tue, 14 Jul 2020 10:40:37: 2000000 INFO @ Tue, 14 Jul 2020 10:40:43: 3000000 INFO @ Tue, 14 Jul 2020 10:40:48: 4000000 INFO @ Tue, 14 Jul 2020 10:40:51: #1 tag size is determined as 58 bps INFO @ Tue, 14 Jul 2020 10:40:51: #1 tag size = 58 INFO @ Tue, 14 Jul 2020 10:40:51: #1 total tags in treatment: 4643122 INFO @ Tue, 14 Jul 2020 10:40:51: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:40:51: #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 10:40:52: #1 tags after filtering in treatment: 4643122 INFO @ Tue, 14 Jul 2020 10:40:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:40:52: #1 finished! INFO @ Tue, 14 Jul 2020 10:40:52: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:40:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:40:52: #2 number of paired peaks: 475 WARNING @ Tue, 14 Jul 2020 10:40:52: Fewer paired peaks (475) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 475 pairs to build model! INFO @ Tue, 14 Jul 2020 10:40:52: start model_add_line... INFO @ Tue, 14 Jul 2020 10:40:52: start X-correlation... INFO @ Tue, 14 Jul 2020 10:40:52: end of X-cor INFO @ Tue, 14 Jul 2020 10:40:52: #2 finished! INFO @ Tue, 14 Jul 2020 10:40:52: #2 predicted fragment length is 61 bps INFO @ Tue, 14 Jul 2020 10:40:52: #2 alternative fragment length(s) may be 61 bps INFO @ Tue, 14 Jul 2020 10:40:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521300/SRX8521300.05_model.r WARNING @ Tue, 14 Jul 2020 10:40:52: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:40:52: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Tue, 14 Jul 2020 10:40:52: #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 10:40:52: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:40:52: #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 10:40:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521300/SRX8521300.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521300/SRX8521300.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521300/SRX8521300.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521300/SRX8521300.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 10:40:57: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:40:57: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:41:02: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:41:03: 1000000 INFO @ Tue, 14 Jul 2020 10:41:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521300/SRX8521300.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:41:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521300/SRX8521300.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:41:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521300/SRX8521300.05_summits.bed INFO @ Tue, 14 Jul 2020 10:41:07: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1798 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:41:09: 2000000 INFO @ Tue, 14 Jul 2020 10:41:16: 3000000 INFO @ Tue, 14 Jul 2020 10:41:22: 4000000 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 10:41:26: #1 tag size is determined as 58 bps INFO @ Tue, 14 Jul 2020 10:41:26: #1 tag size = 58 INFO @ Tue, 14 Jul 2020 10:41:26: #1 total tags in treatment: 4643122 INFO @ Tue, 14 Jul 2020 10:41:26: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:41:26: #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 10:41:26: #1 tags after filtering in treatment: 4643122 INFO @ Tue, 14 Jul 2020 10:41:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:41:26: #1 finished! INFO @ Tue, 14 Jul 2020 10:41:26: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:41:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:41:26: #2 number of paired peaks: 475 WARNING @ Tue, 14 Jul 2020 10:41:26: Fewer paired peaks (475) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 475 pairs to build model! INFO @ Tue, 14 Jul 2020 10:41:26: start model_add_line... INFO @ Tue, 14 Jul 2020 10:41:26: start X-correlation... INFO @ Tue, 14 Jul 2020 10:41:26: end of X-cor INFO @ Tue, 14 Jul 2020 10:41:26: #2 finished! INFO @ Tue, 14 Jul 2020 10:41:26: #2 predicted fragment length is 61 bps INFO @ Tue, 14 Jul 2020 10:41:26: #2 alternative fragment length(s) may be 61 bps INFO @ Tue, 14 Jul 2020 10:41:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521300/SRX8521300.10_model.r WARNING @ Tue, 14 Jul 2020 10:41:26: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:41:26: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Tue, 14 Jul 2020 10:41:26: #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 10:41:26: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:41:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:41:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521300/SRX8521300.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521300/SRX8521300.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521300/SRX8521300.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521300/SRX8521300.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 10:41:27: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:41:27: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:41:32: 1000000 INFO @ Tue, 14 Jul 2020 10:41:36: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:41:37: 2000000 INFO @ Tue, 14 Jul 2020 10:41:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521300/SRX8521300.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:41:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521300/SRX8521300.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:41:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521300/SRX8521300.10_summits.bed INFO @ Tue, 14 Jul 2020 10:41:41: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (711 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:41:43: 3000000 INFO @ Tue, 14 Jul 2020 10:41:48: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:41:52: #1 tag size is determined as 58 bps INFO @ Tue, 14 Jul 2020 10:41:52: #1 tag size = 58 INFO @ Tue, 14 Jul 2020 10:41:52: #1 total tags in treatment: 4643122 INFO @ Tue, 14 Jul 2020 10:41:52: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:41:52: #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 10:41:52: #1 tags after filtering in treatment: 4643122 INFO @ Tue, 14 Jul 2020 10:41:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:41:52: #1 finished! INFO @ Tue, 14 Jul 2020 10:41:52: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:41:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:41:52: #2 number of paired peaks: 475 WARNING @ Tue, 14 Jul 2020 10:41:52: Fewer paired peaks (475) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 475 pairs to build model! INFO @ Tue, 14 Jul 2020 10:41:52: start model_add_line... INFO @ Tue, 14 Jul 2020 10:41:52: start X-correlation... INFO @ Tue, 14 Jul 2020 10:41:52: end of X-cor INFO @ Tue, 14 Jul 2020 10:41:52: #2 finished! INFO @ Tue, 14 Jul 2020 10:41:52: #2 predicted fragment length is 61 bps INFO @ Tue, 14 Jul 2020 10:41:52: #2 alternative fragment length(s) may be 61 bps INFO @ Tue, 14 Jul 2020 10:41:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521300/SRX8521300.20_model.r WARNING @ Tue, 14 Jul 2020 10:41:52: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:41:52: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Tue, 14 Jul 2020 10:41:52: #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 10:41:52: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:41:52: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:42:02: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:42:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521300/SRX8521300.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:42:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521300/SRX8521300.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:42:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521300/SRX8521300.20_summits.bed INFO @ Tue, 14 Jul 2020 10:42:07: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (136 records, 4 fields): 2 millis CompletedMACS2peakCalling