Job ID = 6627249 SRX = SRX8521324 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:36:30 prefetch.2.10.7: 1) Downloading 'SRR11977965'... 2020-07-14T01:36:30 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:37:37 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:37:37 prefetch.2.10.7: 'SRR11977965' is valid 2020-07-14T01:37:37 prefetch.2.10.7: 1) 'SRR11977965' was downloaded successfully 2020-07-14T01:37:37 prefetch.2.10.7: 'SRR11977965' has 0 unresolved dependencies Read 10567299 spots for SRR11977965/SRR11977965.sra Written 10567299 spots for SRR11977965/SRR11977965.sra 2020-07-14T01:38:22 prefetch.2.10.7: 1) Downloading 'SRR11977966'... 2020-07-14T01:38:22 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:40:14 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:40:15 prefetch.2.10.7: 'SRR11977966' is valid 2020-07-14T01:40:15 prefetch.2.10.7: 1) 'SRR11977966' was downloaded successfully 2020-07-14T01:40:15 prefetch.2.10.7: 'SRR11977966' has 0 unresolved dependencies Read 10587554 spots for SRR11977966/SRR11977966.sra Written 10587554 spots for SRR11977966/SRR11977966.sra 2020-07-14T01:41:03 prefetch.2.10.7: 1) Downloading 'SRR11977967'... 2020-07-14T01:41:03 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:42:53 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:42:53 prefetch.2.10.7: 'SRR11977967' is valid 2020-07-14T01:42:53 prefetch.2.10.7: 1) 'SRR11977967' was downloaded successfully 2020-07-14T01:42:53 prefetch.2.10.7: 'SRR11977967' has 0 unresolved dependencies Read 10636839 spots for SRR11977967/SRR11977967.sra Written 10636839 spots for SRR11977967/SRR11977967.sra 2020-07-14T01:43:38 prefetch.2.10.7: 1) Downloading 'SRR11977968'... 2020-07-14T01:43:38 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:44:39 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:44:39 prefetch.2.10.7: 'SRR11977968' is valid 2020-07-14T01:44:39 prefetch.2.10.7: 1) 'SRR11977968' was downloaded successfully 2020-07-14T01:44:39 prefetch.2.10.7: 'SRR11977968' has 0 unresolved dependencies Read 10877811 spots for SRR11977968/SRR11977968.sra Written 10877811 spots for SRR11977968/SRR11977968.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627456 ("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: 00:05:52 42669503 reads; of these: 42669503 (100.00%) were unpaired; of these: 37916523 (88.86%) aligned 0 times 3642489 (8.54%) aligned exactly 1 time 1110491 (2.60%) aligned >1 times 11.14% overall alignment rate Time searching: 00:05:52 Overall time: 00:05:52 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] 777204 / 4752980 = 0.1635 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 10:53:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521324/SRX8521324.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521324/SRX8521324.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521324/SRX8521324.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521324/SRX8521324.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 10:53:09: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:53:09: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:53:14: 1000000 INFO @ Tue, 14 Jul 2020 10:53:19: 2000000 INFO @ Tue, 14 Jul 2020 10:53:24: 3000000 INFO @ Tue, 14 Jul 2020 10:53:30: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 10:53:30: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 10:53:30: #1 total tags in treatment: 3975776 INFO @ Tue, 14 Jul 2020 10:53:30: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:53:30: #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 10:53:30: #1 tags after filtering in treatment: 3975776 INFO @ Tue, 14 Jul 2020 10:53:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:53:30: #1 finished! INFO @ Tue, 14 Jul 2020 10:53:30: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:53:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:53:31: #2 number of paired peaks: 525 WARNING @ Tue, 14 Jul 2020 10:53:31: Fewer paired peaks (525) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 525 pairs to build model! INFO @ Tue, 14 Jul 2020 10:53:31: start model_add_line... INFO @ Tue, 14 Jul 2020 10:53:31: start X-correlation... INFO @ Tue, 14 Jul 2020 10:53:31: end of X-cor INFO @ Tue, 14 Jul 2020 10:53:31: #2 finished! INFO @ Tue, 14 Jul 2020 10:53:31: #2 predicted fragment length is 61 bps INFO @ Tue, 14 Jul 2020 10:53:31: #2 alternative fragment length(s) may be 61 bps INFO @ Tue, 14 Jul 2020 10:53:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521324/SRX8521324.05_model.r WARNING @ Tue, 14 Jul 2020 10:53:31: #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 10:53:31: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Tue, 14 Jul 2020 10:53:31: #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 10:53:31: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:53:31: #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 10:53:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521324/SRX8521324.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521324/SRX8521324.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521324/SRX8521324.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521324/SRX8521324.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 10:53:38: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:53:38: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:53:40: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:53:45: 1000000 INFO @ Tue, 14 Jul 2020 10:53:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521324/SRX8521324.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:53:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521324/SRX8521324.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:53:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521324/SRX8521324.05_summits.bed INFO @ Tue, 14 Jul 2020 10:53:45: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1594 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:53:51: 2000000 INFO @ Tue, 14 Jul 2020 10:53:58: 3000000 INFO @ Tue, 14 Jul 2020 10:54:04: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 10:54:04: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 10:54:04: #1 total tags in treatment: 3975776 INFO @ Tue, 14 Jul 2020 10:54:04: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:54:04: #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 10:54:04: #1 tags after filtering in treatment: 3975776 INFO @ Tue, 14 Jul 2020 10:54:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:54:04: #1 finished! INFO @ Tue, 14 Jul 2020 10:54:04: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:54:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:54:05: #2 number of paired peaks: 525 WARNING @ Tue, 14 Jul 2020 10:54:05: Fewer paired peaks (525) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 525 pairs to build model! INFO @ Tue, 14 Jul 2020 10:54:05: start model_add_line... INFO @ Tue, 14 Jul 2020 10:54:05: start X-correlation... INFO @ Tue, 14 Jul 2020 10:54:05: end of X-cor INFO @ Tue, 14 Jul 2020 10:54:05: #2 finished! INFO @ Tue, 14 Jul 2020 10:54:05: #2 predicted fragment length is 61 bps INFO @ Tue, 14 Jul 2020 10:54:05: #2 alternative fragment length(s) may be 61 bps INFO @ Tue, 14 Jul 2020 10:54:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521324/SRX8521324.10_model.r WARNING @ Tue, 14 Jul 2020 10:54:05: #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 10:54:05: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Tue, 14 Jul 2020 10:54:05: #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 10:54:05: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:54:05: #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 10:54:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521324/SRX8521324.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521324/SRX8521324.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521324/SRX8521324.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521324/SRX8521324.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 10:54:08: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:54:08: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:54:14: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:54:14: 1000000 INFO @ Tue, 14 Jul 2020 10:54:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521324/SRX8521324.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:54:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521324/SRX8521324.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:54:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521324/SRX8521324.10_summits.bed INFO @ Tue, 14 Jul 2020 10:54:18: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (656 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:54:20: 2000000 INFO @ Tue, 14 Jul 2020 10:54:25: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:54:30: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 10:54:30: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 10:54:30: #1 total tags in treatment: 3975776 INFO @ Tue, 14 Jul 2020 10:54:30: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:54:30: #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 10:54:30: #1 tags after filtering in treatment: 3975776 INFO @ Tue, 14 Jul 2020 10:54:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:54:30: #1 finished! INFO @ Tue, 14 Jul 2020 10:54:30: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:54:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:54:31: #2 number of paired peaks: 525 WARNING @ Tue, 14 Jul 2020 10:54:31: Fewer paired peaks (525) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 525 pairs to build model! INFO @ Tue, 14 Jul 2020 10:54:31: start model_add_line... INFO @ Tue, 14 Jul 2020 10:54:31: start X-correlation... INFO @ Tue, 14 Jul 2020 10:54:31: end of X-cor INFO @ Tue, 14 Jul 2020 10:54:31: #2 finished! INFO @ Tue, 14 Jul 2020 10:54:31: #2 predicted fragment length is 61 bps INFO @ Tue, 14 Jul 2020 10:54:31: #2 alternative fragment length(s) may be 61 bps INFO @ Tue, 14 Jul 2020 10:54:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521324/SRX8521324.20_model.r WARNING @ Tue, 14 Jul 2020 10:54:31: #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 10:54:31: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Tue, 14 Jul 2020 10:54:31: #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 10:54:31: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:54:31: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:54:39: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:54:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521324/SRX8521324.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:54:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521324/SRX8521324.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:54:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521324/SRX8521324.20_summits.bed INFO @ Tue, 14 Jul 2020 10:54:43: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (154 records, 4 fields): 1 millis CompletedMACS2peakCalling