Job ID = 6627287 SRX = SRX8521350 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:50:30 prefetch.2.10.7: 1) Downloading 'SRR11978644'... 2020-07-14T01:50:30 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:51:19 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:51:19 prefetch.2.10.7: 'SRR11978644' is valid 2020-07-14T01:51:19 prefetch.2.10.7: 1) 'SRR11978644' was downloaded successfully 2020-07-14T01:51:19 prefetch.2.10.7: 'SRR11978644' has 0 unresolved dependencies Read 9312677 spots for SRR11978644/SRR11978644.sra Written 9312677 spots for SRR11978644/SRR11978644.sra 2020-07-14T01:52:12 prefetch.2.10.7: 1) Downloading 'SRR11978645'... 2020-07-14T01:52:12 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:53:08 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:53:08 prefetch.2.10.7: 'SRR11978645' is valid 2020-07-14T01:53:08 prefetch.2.10.7: 1) 'SRR11978645' was downloaded successfully 2020-07-14T01:53:08 prefetch.2.10.7: 'SRR11978645' has 0 unresolved dependencies Read 9075128 spots for SRR11978645/SRR11978645.sra Written 9075128 spots for SRR11978645/SRR11978645.sra 2020-07-14T01:53:55 prefetch.2.10.7: 1) Downloading 'SRR11978646'... 2020-07-14T01:53:55 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:56:21 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:56:21 prefetch.2.10.7: 'SRR11978646' is valid 2020-07-14T01:56:21 prefetch.2.10.7: 1) 'SRR11978646' was downloaded successfully 2020-07-14T01:56:21 prefetch.2.10.7: 'SRR11978646' has 0 unresolved dependencies Read 9380116 spots for SRR11978646/SRR11978646.sra Written 9380116 spots for SRR11978646/SRR11978646.sra 2020-07-14T01:57:06 prefetch.2.10.7: 1) Downloading 'SRR11978647'... 2020-07-14T01:57:06 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:59:25 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:59:26 prefetch.2.10.7: 'SRR11978647' is valid 2020-07-14T01:59:26 prefetch.2.10.7: 1) 'SRR11978647' was downloaded successfully 2020-07-14T01:59:26 prefetch.2.10.7: 'SRR11978647' has 0 unresolved dependencies Read 9399766 spots for SRR11978647/SRR11978647.sra Written 9399766 spots for SRR11978647/SRR11978647.sra 2020-07-14T02:00:16 prefetch.2.10.7: 1) Downloading 'SRR11978648'... 2020-07-14T02:00:16 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:00:37 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:00:37 prefetch.2.10.7: 'SRR11978648' is valid 2020-07-14T02:00:37 prefetch.2.10.7: 1) 'SRR11978648' was downloaded successfully 2020-07-14T02:00:37 prefetch.2.10.7: 'SRR11978648' has 0 unresolved dependencies Read 876146 spots for SRR11978648/SRR11978648.sra Written 876146 spots for SRR11978648/SRR11978648.sra 2020-07-14T02:00:54 prefetch.2.10.7: 1) Downloading 'SRR11978649'... 2020-07-14T02:00:54 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:01:14 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:01:15 prefetch.2.10.7: 'SRR11978649' is valid 2020-07-14T02:01:15 prefetch.2.10.7: 1) 'SRR11978649' was downloaded successfully 2020-07-14T02:01:15 prefetch.2.10.7: 'SRR11978649' has 0 unresolved dependencies Read 836526 spots for SRR11978649/SRR11978649.sra Written 836526 spots for SRR11978649/SRR11978649.sra 2020-07-14T02:01:42 prefetch.2.10.7: 1) Downloading 'SRR11978650'... 2020-07-14T02:01:42 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:02:24 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:02:24 prefetch.2.10.7: 'SRR11978650' is valid 2020-07-14T02:02:24 prefetch.2.10.7: 1) 'SRR11978650' was downloaded successfully 2020-07-14T02:02:24 prefetch.2.10.7: 'SRR11978650' has 0 unresolved dependencies Read 892385 spots for SRR11978650/SRR11978650.sra Written 892385 spots for SRR11978650/SRR11978650.sra 2020-07-14T02:02:38 prefetch.2.10.7: 1) Downloading 'SRR11978651'... 2020-07-14T02:02:38 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:03:01 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:03:01 prefetch.2.10.7: 'SRR11978651' is valid 2020-07-14T02:03:01 prefetch.2.10.7: 1) 'SRR11978651' was downloaded successfully 2020-07-14T02:03:01 prefetch.2.10.7: 'SRR11978651' has 0 unresolved dependencies Read 873778 spots for SRR11978651/SRR11978651.sra Written 873778 spots for SRR11978651/SRR11978651.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627519 ("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: 00:04:42 40646522 reads; of these: 40646522 (100.00%) were unpaired; of these: 35711428 (87.86%) aligned 0 times 3846043 (9.46%) aligned exactly 1 time 1089051 (2.68%) aligned >1 times 12.14% overall alignment rate Time searching: 00:04:42 Overall time: 00:04:42 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] 1026534 / 4935094 = 0.2080 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 11:09:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521350/SRX8521350.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521350/SRX8521350.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521350/SRX8521350.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521350/SRX8521350.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 11:09:49: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:09:49: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:09:56: 1000000 INFO @ Tue, 14 Jul 2020 11:10:03: 2000000 INFO @ Tue, 14 Jul 2020 11:10:10: 3000000 INFO @ Tue, 14 Jul 2020 11:10:16: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 11:10:16: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 11:10:16: #1 total tags in treatment: 3908560 INFO @ Tue, 14 Jul 2020 11:10:16: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:10:16: #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 11:10:16: #1 tags after filtering in treatment: 3908560 INFO @ Tue, 14 Jul 2020 11:10:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:10:16: #1 finished! INFO @ Tue, 14 Jul 2020 11:10:16: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:10:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:10:16: #2 number of paired peaks: 486 WARNING @ Tue, 14 Jul 2020 11:10:16: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Tue, 14 Jul 2020 11:10:16: start model_add_line... INFO @ Tue, 14 Jul 2020 11:10:16: start X-correlation... INFO @ Tue, 14 Jul 2020 11:10:16: end of X-cor INFO @ Tue, 14 Jul 2020 11:10:16: #2 finished! INFO @ Tue, 14 Jul 2020 11:10:16: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 11:10:16: #2 alternative fragment length(s) may be 58 bps INFO @ Tue, 14 Jul 2020 11:10:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521350/SRX8521350.05_model.r WARNING @ Tue, 14 Jul 2020 11:10:16: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:10:16: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Tue, 14 Jul 2020 11:10:16: #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 11:10:16: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:10:16: #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 11:10:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521350/SRX8521350.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521350/SRX8521350.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521350/SRX8521350.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521350/SRX8521350.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 11:10:19: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:10:19: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:10:25: 1000000 INFO @ Tue, 14 Jul 2020 11:10:25: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:10:30: 2000000 INFO @ Tue, 14 Jul 2020 11:10:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521350/SRX8521350.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:10:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521350/SRX8521350.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:10:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521350/SRX8521350.05_summits.bed INFO @ Tue, 14 Jul 2020 11:10:30: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1401 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:10:35: 3000000 INFO @ Tue, 14 Jul 2020 11:10:40: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 11:10:40: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 11:10:40: #1 total tags in treatment: 3908560 INFO @ Tue, 14 Jul 2020 11:10:40: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:10:40: #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 11:10:40: #1 tags after filtering in treatment: 3908560 INFO @ Tue, 14 Jul 2020 11:10:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:10:40: #1 finished! INFO @ Tue, 14 Jul 2020 11:10:40: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:10:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:10:40: #2 number of paired peaks: 486 WARNING @ Tue, 14 Jul 2020 11:10:40: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Tue, 14 Jul 2020 11:10:40: start model_add_line... INFO @ Tue, 14 Jul 2020 11:10:40: start X-correlation... INFO @ Tue, 14 Jul 2020 11:10:40: end of X-cor INFO @ Tue, 14 Jul 2020 11:10:40: #2 finished! INFO @ Tue, 14 Jul 2020 11:10:40: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 11:10:40: #2 alternative fragment length(s) may be 58 bps INFO @ Tue, 14 Jul 2020 11:10:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521350/SRX8521350.10_model.r WARNING @ Tue, 14 Jul 2020 11:10:40: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:10:40: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Tue, 14 Jul 2020 11:10:40: #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 11:10:40: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:10:40: #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 11:10:49: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:10:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521350/SRX8521350.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521350/SRX8521350.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521350/SRX8521350.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521350/SRX8521350.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 11:10:49: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:10:49: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:10:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521350/SRX8521350.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:10:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521350/SRX8521350.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:10:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521350/SRX8521350.10_summits.bed INFO @ Tue, 14 Jul 2020 11:10:53: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (500 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:10:55: 1000000 INFO @ Tue, 14 Jul 2020 11:11:02: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:11:08: 3000000 INFO @ Tue, 14 Jul 2020 11:11:14: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 11:11:14: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 11:11:14: #1 total tags in treatment: 3908560 INFO @ Tue, 14 Jul 2020 11:11:14: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:11:14: #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 11:11:14: #1 tags after filtering in treatment: 3908560 INFO @ Tue, 14 Jul 2020 11:11:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:11:14: #1 finished! INFO @ Tue, 14 Jul 2020 11:11:14: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:11:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:11:14: #2 number of paired peaks: 486 WARNING @ Tue, 14 Jul 2020 11:11:14: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Tue, 14 Jul 2020 11:11:14: start model_add_line... INFO @ Tue, 14 Jul 2020 11:11:14: start X-correlation... INFO @ Tue, 14 Jul 2020 11:11:14: end of X-cor INFO @ Tue, 14 Jul 2020 11:11:14: #2 finished! INFO @ Tue, 14 Jul 2020 11:11:14: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 11:11:14: #2 alternative fragment length(s) may be 58 bps INFO @ Tue, 14 Jul 2020 11:11:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521350/SRX8521350.20_model.r WARNING @ Tue, 14 Jul 2020 11:11:14: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:11:14: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Tue, 14 Jul 2020 11:11:14: #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 11:11:14: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:11:14: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:11:22: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:11:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521350/SRX8521350.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:11:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521350/SRX8521350.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:11:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521350/SRX8521350.20_summits.bed INFO @ Tue, 14 Jul 2020 11:11:26: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (105 records, 4 fields): 1 millis CompletedMACS2peakCalling