Job ID = 6627460 SRX = SRX8521386 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T02:37:24 prefetch.2.10.7: 1) Downloading 'SRR11978286'... 2020-07-14T02:37:24 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:38:23 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:38:24 prefetch.2.10.7: 'SRR11978286' is valid 2020-07-14T02:38:24 prefetch.2.10.7: 1) 'SRR11978286' was downloaded successfully 2020-07-14T02:38:24 prefetch.2.10.7: 'SRR11978286' has 0 unresolved dependencies Read 11620572 spots for SRR11978286/SRR11978286.sra Written 11620572 spots for SRR11978286/SRR11978286.sra 2020-07-14T02:39:21 prefetch.2.10.7: 1) Downloading 'SRR11978287'... 2020-07-14T02:39:21 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:40:46 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:40:46 prefetch.2.10.7: 'SRR11978287' is valid 2020-07-14T02:40:46 prefetch.2.10.7: 1) 'SRR11978287' was downloaded successfully 2020-07-14T02:40:46 prefetch.2.10.7: 'SRR11978287' has 0 unresolved dependencies Read 11475604 spots for SRR11978287/SRR11978287.sra Written 11475604 spots for SRR11978287/SRR11978287.sra 2020-07-14T02:41:42 prefetch.2.10.7: 1) Downloading 'SRR11978288'... 2020-07-14T02:41:42 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:42:54 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:42:54 prefetch.2.10.7: 'SRR11978288' is valid 2020-07-14T02:42:54 prefetch.2.10.7: 1) 'SRR11978288' was downloaded successfully 2020-07-14T02:42:54 prefetch.2.10.7: 'SRR11978288' has 0 unresolved dependencies Read 11469644 spots for SRR11978288/SRR11978288.sra Written 11469644 spots for SRR11978288/SRR11978288.sra 2020-07-14T02:43:50 prefetch.2.10.7: 1) Downloading 'SRR11978289'... 2020-07-14T02:43:50 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:45:01 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:45:01 prefetch.2.10.7: 'SRR11978289' is valid 2020-07-14T02:45:01 prefetch.2.10.7: 1) 'SRR11978289' was downloaded successfully 2020-07-14T02:45:01 prefetch.2.10.7: 'SRR11978289' has 0 unresolved dependencies Read 11503767 spots for SRR11978289/SRR11978289.sra Written 11503767 spots for SRR11978289/SRR11978289.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627657 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:54 46069587 reads; of these: 46069587 (100.00%) were unpaired; of these: 42147113 (91.49%) aligned 0 times 2922551 (6.34%) aligned exactly 1 time 999923 (2.17%) aligned >1 times 8.51% overall alignment rate Time searching: 00:07:55 Overall time: 00:07:55 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] 761083 / 3922474 = 0.1940 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 11:55:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521386/SRX8521386.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521386/SRX8521386.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521386/SRX8521386.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521386/SRX8521386.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 11:55:32: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:55:32: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:55:39: 1000000 INFO @ Tue, 14 Jul 2020 11:55:47: 2000000 INFO @ Tue, 14 Jul 2020 11:55:54: 3000000 INFO @ Tue, 14 Jul 2020 11:55:56: #1 tag size is determined as 66 bps INFO @ Tue, 14 Jul 2020 11:55:56: #1 tag size = 66 INFO @ Tue, 14 Jul 2020 11:55:56: #1 total tags in treatment: 3161391 INFO @ Tue, 14 Jul 2020 11:55:56: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:55:56: #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 11:55:56: #1 tags after filtering in treatment: 3161391 INFO @ Tue, 14 Jul 2020 11:55:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:55:56: #1 finished! INFO @ Tue, 14 Jul 2020 11:55:56: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:55:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:55:56: #2 number of paired peaks: 692 WARNING @ Tue, 14 Jul 2020 11:55:56: Fewer paired peaks (692) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 692 pairs to build model! INFO @ Tue, 14 Jul 2020 11:55:56: start model_add_line... INFO @ Tue, 14 Jul 2020 11:55:56: start X-correlation... INFO @ Tue, 14 Jul 2020 11:55:56: end of X-cor INFO @ Tue, 14 Jul 2020 11:55:56: #2 finished! INFO @ Tue, 14 Jul 2020 11:55:56: #2 predicted fragment length is 62 bps INFO @ Tue, 14 Jul 2020 11:55:56: #2 alternative fragment length(s) may be 62 bps INFO @ Tue, 14 Jul 2020 11:55:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521386/SRX8521386.05_model.r WARNING @ Tue, 14 Jul 2020 11:55:56: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:55:56: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Tue, 14 Jul 2020 11:55:56: #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 11:55:56: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:55:56: #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 11:56:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521386/SRX8521386.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521386/SRX8521386.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521386/SRX8521386.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521386/SRX8521386.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 11:56:02: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:56:02: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:56:04: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:56:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521386/SRX8521386.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:56:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521386/SRX8521386.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:56:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521386/SRX8521386.05_summits.bed INFO @ Tue, 14 Jul 2020 11:56:08: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1475 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:56:09: 1000000 INFO @ Tue, 14 Jul 2020 11:56:17: 2000000 INFO @ Tue, 14 Jul 2020 11:56:24: 3000000 INFO @ Tue, 14 Jul 2020 11:56:25: #1 tag size is determined as 66 bps INFO @ Tue, 14 Jul 2020 11:56:25: #1 tag size = 66 INFO @ Tue, 14 Jul 2020 11:56:25: #1 total tags in treatment: 3161391 INFO @ Tue, 14 Jul 2020 11:56:25: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:56:25: #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 11:56:25: #1 tags after filtering in treatment: 3161391 INFO @ Tue, 14 Jul 2020 11:56:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:56:25: #1 finished! INFO @ Tue, 14 Jul 2020 11:56:25: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:56:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:56:26: #2 number of paired peaks: 692 WARNING @ Tue, 14 Jul 2020 11:56:26: Fewer paired peaks (692) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 692 pairs to build model! INFO @ Tue, 14 Jul 2020 11:56:26: start model_add_line... INFO @ Tue, 14 Jul 2020 11:56:26: start X-correlation... INFO @ Tue, 14 Jul 2020 11:56:26: end of X-cor INFO @ Tue, 14 Jul 2020 11:56:26: #2 finished! INFO @ Tue, 14 Jul 2020 11:56:26: #2 predicted fragment length is 62 bps INFO @ Tue, 14 Jul 2020 11:56:26: #2 alternative fragment length(s) may be 62 bps INFO @ Tue, 14 Jul 2020 11:56:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521386/SRX8521386.10_model.r WARNING @ Tue, 14 Jul 2020 11:56:26: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:56:26: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Tue, 14 Jul 2020 11:56:26: #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 11:56:26: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:56:26: #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 11:56:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521386/SRX8521386.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521386/SRX8521386.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521386/SRX8521386.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521386/SRX8521386.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 11:56:32: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:56:32: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:56:33: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:56:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521386/SRX8521386.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:56:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521386/SRX8521386.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:56:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521386/SRX8521386.10_summits.bed INFO @ Tue, 14 Jul 2020 11:56:37: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (604 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:56:40: 1000000 INFO @ Tue, 14 Jul 2020 11:56:48: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:56:56: 3000000 INFO @ Tue, 14 Jul 2020 11:56:57: #1 tag size is determined as 66 bps INFO @ Tue, 14 Jul 2020 11:56:57: #1 tag size = 66 INFO @ Tue, 14 Jul 2020 11:56:57: #1 total tags in treatment: 3161391 INFO @ Tue, 14 Jul 2020 11:56:57: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:56:57: #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 11:56:57: #1 tags after filtering in treatment: 3161391 INFO @ Tue, 14 Jul 2020 11:56:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:56:57: #1 finished! INFO @ Tue, 14 Jul 2020 11:56:57: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:56:57: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:56:57: #2 number of paired peaks: 692 WARNING @ Tue, 14 Jul 2020 11:56:57: Fewer paired peaks (692) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 692 pairs to build model! INFO @ Tue, 14 Jul 2020 11:56:57: start model_add_line... INFO @ Tue, 14 Jul 2020 11:56:57: start X-correlation... INFO @ Tue, 14 Jul 2020 11:56:57: end of X-cor INFO @ Tue, 14 Jul 2020 11:56:57: #2 finished! INFO @ Tue, 14 Jul 2020 11:56:57: #2 predicted fragment length is 62 bps INFO @ Tue, 14 Jul 2020 11:56:57: #2 alternative fragment length(s) may be 62 bps INFO @ Tue, 14 Jul 2020 11:56:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521386/SRX8521386.20_model.r WARNING @ Tue, 14 Jul 2020 11:56:57: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:56:57: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Tue, 14 Jul 2020 11:56:57: #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 11:56:57: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:56:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:57:05: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:57:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521386/SRX8521386.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:57:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521386/SRX8521386.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:57:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521386/SRX8521386.20_summits.bed INFO @ Tue, 14 Jul 2020 11:57:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (144 records, 4 fields): 2 millis CompletedMACS2peakCalling