Job ID = 6627170 SRX = SRX8521304 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:26:04 prefetch.2.10.7: 1) Downloading 'SRR11978665'... 2020-07-14T01:26:04 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:27:19 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:27:20 prefetch.2.10.7: 'SRR11978665' is valid 2020-07-14T01:27:20 prefetch.2.10.7: 1) 'SRR11978665' was downloaded successfully 2020-07-14T01:27:20 prefetch.2.10.7: 'SRR11978665' has 0 unresolved dependencies Read 8950401 spots for SRR11978665/SRR11978665.sra Written 8950401 spots for SRR11978665/SRR11978665.sra 2020-07-14T01:28:04 prefetch.2.10.7: 1) Downloading 'SRR11978666'... 2020-07-14T01:28:04 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:29:43 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:29:43 prefetch.2.10.7: 'SRR11978666' is valid 2020-07-14T01:29:43 prefetch.2.10.7: 1) 'SRR11978666' was downloaded successfully 2020-07-14T01:29:43 prefetch.2.10.7: 'SRR11978666' has 0 unresolved dependencies Read 8853917 spots for SRR11978666/SRR11978666.sra Written 8853917 spots for SRR11978666/SRR11978666.sra 2020-07-14T01:30:28 prefetch.2.10.7: 1) Downloading 'SRR11978667'... 2020-07-14T01:30:28 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:31:35 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:31:36 prefetch.2.10.7: 'SRR11978667' is valid 2020-07-14T01:31:36 prefetch.2.10.7: 1) 'SRR11978667' was downloaded successfully 2020-07-14T01:31:36 prefetch.2.10.7: 'SRR11978667' has 0 unresolved dependencies Read 9332905 spots for SRR11978667/SRR11978667.sra Written 9332905 spots for SRR11978667/SRR11978667.sra 2020-07-14T01:32:17 prefetch.2.10.7: 1) Downloading 'SRR11978668'... 2020-07-14T01:32:17 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:33:14 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:33:15 prefetch.2.10.7: 'SRR11978668' is valid 2020-07-14T01:33:15 prefetch.2.10.7: 1) 'SRR11978668' was downloaded successfully 2020-07-14T01:33:15 prefetch.2.10.7: 'SRR11978668' has 0 unresolved dependencies Read 9302954 spots for SRR11978668/SRR11978668.sra Written 9302954 spots for SRR11978668/SRR11978668.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627421 ("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: 00:05:54 36440177 reads; of these: 36440177 (100.00%) were unpaired; of these: 29513629 (80.99%) aligned 0 times 5167098 (14.18%) aligned exactly 1 time 1759450 (4.83%) aligned >1 times 19.01% overall alignment rate Time searching: 00:05:55 Overall time: 00:05:55 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] 1133168 / 6926548 = 0.1636 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 10:42:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521304/SRX8521304.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521304/SRX8521304.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521304/SRX8521304.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521304/SRX8521304.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 10:42:19: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:42:19: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:42:25: 1000000 INFO @ Tue, 14 Jul 2020 10:42:30: 2000000 INFO @ Tue, 14 Jul 2020 10:42:36: 3000000 INFO @ Tue, 14 Jul 2020 10:42:41: 4000000 INFO @ Tue, 14 Jul 2020 10:42:46: 5000000 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 10:42:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521304/SRX8521304.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521304/SRX8521304.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521304/SRX8521304.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521304/SRX8521304.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 10:42:48: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:42:48: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:42:51: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 10:42:51: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 10:42:51: #1 total tags in treatment: 5793380 INFO @ Tue, 14 Jul 2020 10:42:51: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:42:51: #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 10:42:51: #1 tags after filtering in treatment: 5793380 INFO @ Tue, 14 Jul 2020 10:42:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:42:51: #1 finished! INFO @ Tue, 14 Jul 2020 10:42:51: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:42:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:42:52: #2 number of paired peaks: 396 WARNING @ Tue, 14 Jul 2020 10:42:52: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Tue, 14 Jul 2020 10:42:52: start model_add_line... INFO @ Tue, 14 Jul 2020 10:42:52: start X-correlation... INFO @ Tue, 14 Jul 2020 10:42:52: end of X-cor INFO @ Tue, 14 Jul 2020 10:42:52: #2 finished! INFO @ Tue, 14 Jul 2020 10:42:52: #2 predicted fragment length is 59 bps INFO @ Tue, 14 Jul 2020 10:42:52: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 14 Jul 2020 10:42:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521304/SRX8521304.05_model.r WARNING @ Tue, 14 Jul 2020 10:42:52: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:42:52: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 14 Jul 2020 10:42:52: #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 10:42:52: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:42:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:42:55: 1000000 INFO @ Tue, 14 Jul 2020 10:43:01: 2000000 INFO @ Tue, 14 Jul 2020 10:43:04: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:43:07: 3000000 INFO @ Tue, 14 Jul 2020 10:43:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521304/SRX8521304.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:43:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521304/SRX8521304.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:43:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521304/SRX8521304.05_summits.bed INFO @ Tue, 14 Jul 2020 10:43:10: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1944 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:43:14: 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 10:43:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521304/SRX8521304.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521304/SRX8521304.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521304/SRX8521304.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521304/SRX8521304.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 10:43:18: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:43:18: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:43:20: 5000000 INFO @ Tue, 14 Jul 2020 10:43:24: 1000000 INFO @ Tue, 14 Jul 2020 10:43:26: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 10:43:26: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 10:43:26: #1 total tags in treatment: 5793380 INFO @ Tue, 14 Jul 2020 10:43:26: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:43:26: #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 10:43:26: #1 tags after filtering in treatment: 5793380 INFO @ Tue, 14 Jul 2020 10:43:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:43:26: #1 finished! INFO @ Tue, 14 Jul 2020 10:43:26: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:43:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:43:26: #2 number of paired peaks: 396 WARNING @ Tue, 14 Jul 2020 10:43:26: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Tue, 14 Jul 2020 10:43:26: start model_add_line... INFO @ Tue, 14 Jul 2020 10:43:26: start X-correlation... INFO @ Tue, 14 Jul 2020 10:43:26: end of X-cor INFO @ Tue, 14 Jul 2020 10:43:26: #2 finished! INFO @ Tue, 14 Jul 2020 10:43:26: #2 predicted fragment length is 59 bps INFO @ Tue, 14 Jul 2020 10:43:26: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 14 Jul 2020 10:43:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521304/SRX8521304.10_model.r WARNING @ Tue, 14 Jul 2020 10:43:26: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:43:26: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 14 Jul 2020 10:43:26: #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 10:43:26: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:43:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:43:30: 2000000 INFO @ Tue, 14 Jul 2020 10:43:36: 3000000 INFO @ Tue, 14 Jul 2020 10:43:38: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:43:42: 4000000 INFO @ Tue, 14 Jul 2020 10:43:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521304/SRX8521304.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:43:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521304/SRX8521304.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:43:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521304/SRX8521304.10_summits.bed INFO @ Tue, 14 Jul 2020 10:43:44: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (652 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:43:48: 5000000 INFO @ Tue, 14 Jul 2020 10:43:52: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 10:43:52: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 10:43:52: #1 total tags in treatment: 5793380 INFO @ Tue, 14 Jul 2020 10:43:52: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:43:52: #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 10:43:53: #1 tags after filtering in treatment: 5793380 INFO @ Tue, 14 Jul 2020 10:43:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:43:53: #1 finished! INFO @ Tue, 14 Jul 2020 10:43:53: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:43:53: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:43:53: #2 number of paired peaks: 396 WARNING @ Tue, 14 Jul 2020 10:43:53: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Tue, 14 Jul 2020 10:43:53: start model_add_line... INFO @ Tue, 14 Jul 2020 10:43:53: start X-correlation... INFO @ Tue, 14 Jul 2020 10:43:53: end of X-cor INFO @ Tue, 14 Jul 2020 10:43:53: #2 finished! INFO @ Tue, 14 Jul 2020 10:43:53: #2 predicted fragment length is 59 bps INFO @ Tue, 14 Jul 2020 10:43:53: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 14 Jul 2020 10:43:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521304/SRX8521304.20_model.r WARNING @ Tue, 14 Jul 2020 10:43:53: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:43:53: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 14 Jul 2020 10:43:53: #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 10:43:53: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:43:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:44:05: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:44:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521304/SRX8521304.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:44:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521304/SRX8521304.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:44:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521304/SRX8521304.20_summits.bed INFO @ Tue, 14 Jul 2020 10:44:11: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (155 records, 4 fields): 1 millis CompletedMACS2peakCalling