Job ID = 6627321 SRX = SRX8521369 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:57:51 prefetch.2.10.7: 1) Downloading 'SRR11978142'... 2020-07-14T01:57:51 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:59:29 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:59:30 prefetch.2.10.7: 'SRR11978142' is valid 2020-07-14T01:59:30 prefetch.2.10.7: 1) 'SRR11978142' was downloaded successfully 2020-07-14T01:59:30 prefetch.2.10.7: 'SRR11978142' has 0 unresolved dependencies Read 10488018 spots for SRR11978142/SRR11978142.sra Written 10488018 spots for SRR11978142/SRR11978142.sra 2020-07-14T02:00:15 prefetch.2.10.7: 1) Downloading 'SRR11978143'... 2020-07-14T02:00:15 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:01:40 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:01:40 prefetch.2.10.7: 'SRR11978143' is valid 2020-07-14T02:01:40 prefetch.2.10.7: 1) 'SRR11978143' was downloaded successfully 2020-07-14T02:01:40 prefetch.2.10.7: 'SRR11978143' has 0 unresolved dependencies Read 9664592 spots for SRR11978143/SRR11978143.sra Written 9664592 spots for SRR11978143/SRR11978143.sra 2020-07-14T02:02:23 prefetch.2.10.7: 1) Downloading 'SRR11978144'... 2020-07-14T02:02:23 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:03:35 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:03:35 prefetch.2.10.7: 'SRR11978144' is valid 2020-07-14T02:03:35 prefetch.2.10.7: 1) 'SRR11978144' was downloaded successfully 2020-07-14T02:03:35 prefetch.2.10.7: 'SRR11978144' has 0 unresolved dependencies Read 10076247 spots for SRR11978144/SRR11978144.sra Written 10076247 spots for SRR11978144/SRR11978144.sra 2020-07-14T02:04:22 prefetch.2.10.7: 1) Downloading 'SRR11978145'... 2020-07-14T02:04:22 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:06:32 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:06:32 prefetch.2.10.7: 'SRR11978145' is valid 2020-07-14T02:06:32 prefetch.2.10.7: 1) 'SRR11978145' was downloaded successfully 2020-07-14T02:06:32 prefetch.2.10.7: 'SRR11978145' has 0 unresolved dependencies Read 10121306 spots for SRR11978145/SRR11978145.sra Written 10121306 spots for SRR11978145/SRR11978145.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627533 ("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: 00:06:03 40350163 reads; of these: 40350163 (100.00%) were unpaired; of these: 34765602 (86.16%) aligned 0 times 4142096 (10.27%) aligned exactly 1 time 1442465 (3.57%) aligned >1 times 13.84% overall alignment rate Time searching: 00:06:03 Overall time: 00:06:03 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] 972442 / 5584561 = 0.1741 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 11:15:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521369/SRX8521369.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521369/SRX8521369.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521369/SRX8521369.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521369/SRX8521369.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 11:15:27: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:15:27: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:15:33: 1000000 INFO @ Tue, 14 Jul 2020 11:15:40: 2000000 INFO @ Tue, 14 Jul 2020 11:15:47: 3000000 INFO @ Tue, 14 Jul 2020 11:15:53: 4000000 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 11:15:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521369/SRX8521369.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521369/SRX8521369.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521369/SRX8521369.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521369/SRX8521369.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 11:15:57: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:15:57: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:15:58: #1 tag size is determined as 61 bps INFO @ Tue, 14 Jul 2020 11:15:58: #1 tag size = 61 INFO @ Tue, 14 Jul 2020 11:15:58: #1 total tags in treatment: 4612119 INFO @ Tue, 14 Jul 2020 11:15:58: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:15:58: #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 11:15:58: #1 tags after filtering in treatment: 4612119 INFO @ Tue, 14 Jul 2020 11:15:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:15:58: #1 finished! INFO @ Tue, 14 Jul 2020 11:15:58: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:15:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:15:58: #2 number of paired peaks: 434 WARNING @ Tue, 14 Jul 2020 11:15:58: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Tue, 14 Jul 2020 11:15:58: start model_add_line... INFO @ Tue, 14 Jul 2020 11:15:58: start X-correlation... INFO @ Tue, 14 Jul 2020 11:15:58: end of X-cor INFO @ Tue, 14 Jul 2020 11:15:58: #2 finished! INFO @ Tue, 14 Jul 2020 11:15:58: #2 predicted fragment length is 61 bps INFO @ Tue, 14 Jul 2020 11:15:58: #2 alternative fragment length(s) may be 61 bps INFO @ Tue, 14 Jul 2020 11:15:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521369/SRX8521369.05_model.r WARNING @ Tue, 14 Jul 2020 11:15:58: #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 11:15:58: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Tue, 14 Jul 2020 11:15:58: #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 11:15:58: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:15:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:16:03: 1000000 INFO @ Tue, 14 Jul 2020 11:16:08: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:16:10: 2000000 INFO @ Tue, 14 Jul 2020 11:16:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521369/SRX8521369.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:16:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521369/SRX8521369.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:16:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521369/SRX8521369.05_summits.bed INFO @ Tue, 14 Jul 2020 11:16:13: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1587 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:16:16: 3000000 INFO @ Tue, 14 Jul 2020 11:16:22: 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 11:16:26: #1 tag size is determined as 61 bps INFO @ Tue, 14 Jul 2020 11:16:26: #1 tag size = 61 INFO @ Tue, 14 Jul 2020 11:16:26: #1 total tags in treatment: 4612119 INFO @ Tue, 14 Jul 2020 11:16:26: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:16:26: #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 11:16:26: #1 tags after filtering in treatment: 4612119 INFO @ Tue, 14 Jul 2020 11:16:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:16:26: #1 finished! INFO @ Tue, 14 Jul 2020 11:16:26: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:16:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:16:27: #2 number of paired peaks: 434 WARNING @ Tue, 14 Jul 2020 11:16:27: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Tue, 14 Jul 2020 11:16:27: start model_add_line... INFO @ Tue, 14 Jul 2020 11:16:27: start X-correlation... INFO @ Tue, 14 Jul 2020 11:16:27: end of X-cor INFO @ Tue, 14 Jul 2020 11:16:27: #2 finished! INFO @ Tue, 14 Jul 2020 11:16:27: #2 predicted fragment length is 61 bps INFO @ Tue, 14 Jul 2020 11:16:27: #2 alternative fragment length(s) may be 61 bps INFO @ Tue, 14 Jul 2020 11:16:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521369/SRX8521369.10_model.r WARNING @ Tue, 14 Jul 2020 11:16:27: #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 11:16:27: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Tue, 14 Jul 2020 11:16:27: #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 11:16:27: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:16:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:16:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521369/SRX8521369.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521369/SRX8521369.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521369/SRX8521369.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521369/SRX8521369.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 11:16:27: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:16:27: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:16:33: 1000000 INFO @ Tue, 14 Jul 2020 11:16:36: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:16:39: 2000000 INFO @ Tue, 14 Jul 2020 11:16:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521369/SRX8521369.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:16:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521369/SRX8521369.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:16:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521369/SRX8521369.10_summits.bed INFO @ Tue, 14 Jul 2020 11:16:41: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (610 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:16:45: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:16:51: 4000000 INFO @ Tue, 14 Jul 2020 11:16:55: #1 tag size is determined as 61 bps INFO @ Tue, 14 Jul 2020 11:16:55: #1 tag size = 61 INFO @ Tue, 14 Jul 2020 11:16:55: #1 total tags in treatment: 4612119 INFO @ Tue, 14 Jul 2020 11:16:55: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:16:55: #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 11:16:55: #1 tags after filtering in treatment: 4612119 INFO @ Tue, 14 Jul 2020 11:16:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:16:55: #1 finished! INFO @ Tue, 14 Jul 2020 11:16:55: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:16:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:16:55: #2 number of paired peaks: 434 WARNING @ Tue, 14 Jul 2020 11:16:55: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Tue, 14 Jul 2020 11:16:55: start model_add_line... INFO @ Tue, 14 Jul 2020 11:16:55: start X-correlation... INFO @ Tue, 14 Jul 2020 11:16:55: end of X-cor INFO @ Tue, 14 Jul 2020 11:16:55: #2 finished! INFO @ Tue, 14 Jul 2020 11:16:55: #2 predicted fragment length is 61 bps INFO @ Tue, 14 Jul 2020 11:16:55: #2 alternative fragment length(s) may be 61 bps INFO @ Tue, 14 Jul 2020 11:16:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521369/SRX8521369.20_model.r WARNING @ Tue, 14 Jul 2020 11:16:55: #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 11:16:55: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Tue, 14 Jul 2020 11:16:55: #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 11:16:55: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:16:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:17:05: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:17:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521369/SRX8521369.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:17:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521369/SRX8521369.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:17:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521369/SRX8521369.20_summits.bed INFO @ Tue, 14 Jul 2020 11:17:10: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (147 records, 4 fields): 1 millis CompletedMACS2peakCalling