Job ID = 6627502 SRX = SRX8521395 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T02:45:13 prefetch.2.10.7: 1) Downloading 'SRR11978322'... 2020-07-14T02:45:13 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:47:31 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:47:32 prefetch.2.10.7: 'SRR11978322' is valid 2020-07-14T02:47:32 prefetch.2.10.7: 1) 'SRR11978322' was downloaded successfully 2020-07-14T02:47:32 prefetch.2.10.7: 'SRR11978322' has 0 unresolved dependencies Read 10048685 spots for SRR11978322/SRR11978322.sra Written 10048685 spots for SRR11978322/SRR11978322.sra 2020-07-14T02:48:15 prefetch.2.10.7: 1) Downloading 'SRR11978323'... 2020-07-14T02:48:15 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:49:24 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:49:25 prefetch.2.10.7: 'SRR11978323' is valid 2020-07-14T02:49:25 prefetch.2.10.7: 1) 'SRR11978323' was downloaded successfully 2020-07-14T02:49:25 prefetch.2.10.7: 'SRR11978323' has 0 unresolved dependencies Read 10064546 spots for SRR11978323/SRR11978323.sra Written 10064546 spots for SRR11978323/SRR11978323.sra 2020-07-14T02:50:12 prefetch.2.10.7: 1) Downloading 'SRR11978324'... 2020-07-14T02:50:12 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:51:16 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:51:17 prefetch.2.10.7: 'SRR11978324' is valid 2020-07-14T02:51:17 prefetch.2.10.7: 1) 'SRR11978324' was downloaded successfully 2020-07-14T02:51:17 prefetch.2.10.7: 'SRR11978324' has 0 unresolved dependencies Read 9991687 spots for SRR11978324/SRR11978324.sra Written 9991687 spots for SRR11978324/SRR11978324.sra 2020-07-14T02:51:59 prefetch.2.10.7: 1) Downloading 'SRR11978325'... 2020-07-14T02:51:59 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:53:07 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:53:08 prefetch.2.10.7: 'SRR11978325' is valid 2020-07-14T02:53:08 prefetch.2.10.7: 1) 'SRR11978325' was downloaded successfully 2020-07-14T02:53:08 prefetch.2.10.7: 'SRR11978325' has 0 unresolved dependencies Read 9987270 spots for SRR11978325/SRR11978325.sra Written 9987270 spots for SRR11978325/SRR11978325.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627681 ("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: 00:05:28 40092188 reads; of these: 40092188 (100.00%) were unpaired; of these: 34746072 (86.67%) aligned 0 times 4113921 (10.26%) aligned exactly 1 time 1232195 (3.07%) aligned >1 times 13.33% overall alignment rate Time searching: 00:05:28 Overall time: 00:05:28 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] 732412 / 5346116 = 0.1370 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 12:01:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521395/SRX8521395.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521395/SRX8521395.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521395/SRX8521395.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521395/SRX8521395.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 12:01:22: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:01:22: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:01:28: 1000000 INFO @ Tue, 14 Jul 2020 12:01:33: 2000000 INFO @ Tue, 14 Jul 2020 12:01:39: 3000000 INFO @ Tue, 14 Jul 2020 12:01:45: 4000000 INFO @ Tue, 14 Jul 2020 12:01:48: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 12:01:48: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 12:01:48: #1 total tags in treatment: 4613704 INFO @ Tue, 14 Jul 2020 12:01:48: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:01:48: #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 12:01:48: #1 tags after filtering in treatment: 4613704 INFO @ Tue, 14 Jul 2020 12:01:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:01:48: #1 finished! INFO @ Tue, 14 Jul 2020 12:01:48: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:01:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:01:48: #2 number of paired peaks: 375 WARNING @ Tue, 14 Jul 2020 12:01:48: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Tue, 14 Jul 2020 12:01:48: start model_add_line... INFO @ Tue, 14 Jul 2020 12:01:48: start X-correlation... INFO @ Tue, 14 Jul 2020 12:01:48: end of X-cor INFO @ Tue, 14 Jul 2020 12:01:48: #2 finished! INFO @ Tue, 14 Jul 2020 12:01:48: #2 predicted fragment length is 56 bps INFO @ Tue, 14 Jul 2020 12:01:48: #2 alternative fragment length(s) may be 56 bps INFO @ Tue, 14 Jul 2020 12:01:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521395/SRX8521395.05_model.r WARNING @ Tue, 14 Jul 2020 12:01:48: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:01:48: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Tue, 14 Jul 2020 12:01:48: #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 12:01:48: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:01:48: #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 12:01:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521395/SRX8521395.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521395/SRX8521395.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521395/SRX8521395.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521395/SRX8521395.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 12:01:52: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:01:52: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:01:58: 1000000 INFO @ Tue, 14 Jul 2020 12:01:58: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:02:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521395/SRX8521395.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:02:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521395/SRX8521395.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:02:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521395/SRX8521395.05_summits.bed INFO @ Tue, 14 Jul 2020 12:02:03: Done! INFO @ Tue, 14 Jul 2020 12:02:03: 2000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1135 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:02:09: 3000000 INFO @ Tue, 14 Jul 2020 12:02:15: 4000000 INFO @ Tue, 14 Jul 2020 12:02:18: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 12:02:18: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 12:02:18: #1 total tags in treatment: 4613704 INFO @ Tue, 14 Jul 2020 12:02:18: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:02:18: #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 12:02:18: #1 tags after filtering in treatment: 4613704 INFO @ Tue, 14 Jul 2020 12:02:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:02:18: #1 finished! INFO @ Tue, 14 Jul 2020 12:02:18: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:02:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:02:18: #2 number of paired peaks: 375 WARNING @ Tue, 14 Jul 2020 12:02:18: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Tue, 14 Jul 2020 12:02:18: start model_add_line... INFO @ Tue, 14 Jul 2020 12:02:18: start X-correlation... INFO @ Tue, 14 Jul 2020 12:02:18: end of X-cor INFO @ Tue, 14 Jul 2020 12:02:18: #2 finished! INFO @ Tue, 14 Jul 2020 12:02:18: #2 predicted fragment length is 56 bps INFO @ Tue, 14 Jul 2020 12:02:18: #2 alternative fragment length(s) may be 56 bps INFO @ Tue, 14 Jul 2020 12:02:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521395/SRX8521395.10_model.r WARNING @ Tue, 14 Jul 2020 12:02:18: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:02:18: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Tue, 14 Jul 2020 12:02:18: #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 12:02:18: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:02:18: #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 12:02:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521395/SRX8521395.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521395/SRX8521395.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521395/SRX8521395.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521395/SRX8521395.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 12:02:22: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:02:22: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:02:28: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:02:29: 1000000 INFO @ Tue, 14 Jul 2020 12:02:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521395/SRX8521395.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:02:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521395/SRX8521395.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:02:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521395/SRX8521395.10_summits.bed INFO @ Tue, 14 Jul 2020 12:02:33: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (447 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:02:36: 2000000 INFO @ Tue, 14 Jul 2020 12:02:43: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:02:50: 4000000 INFO @ Tue, 14 Jul 2020 12:02:54: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 12:02:54: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 12:02:54: #1 total tags in treatment: 4613704 INFO @ Tue, 14 Jul 2020 12:02:54: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:02:54: #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 12:02:54: #1 tags after filtering in treatment: 4613704 INFO @ Tue, 14 Jul 2020 12:02:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:02:54: #1 finished! INFO @ Tue, 14 Jul 2020 12:02:54: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:02:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:02:54: #2 number of paired peaks: 375 WARNING @ Tue, 14 Jul 2020 12:02:54: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Tue, 14 Jul 2020 12:02:54: start model_add_line... INFO @ Tue, 14 Jul 2020 12:02:54: start X-correlation... INFO @ Tue, 14 Jul 2020 12:02:54: end of X-cor INFO @ Tue, 14 Jul 2020 12:02:54: #2 finished! INFO @ Tue, 14 Jul 2020 12:02:54: #2 predicted fragment length is 56 bps INFO @ Tue, 14 Jul 2020 12:02:54: #2 alternative fragment length(s) may be 56 bps INFO @ Tue, 14 Jul 2020 12:02:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521395/SRX8521395.20_model.r WARNING @ Tue, 14 Jul 2020 12:02:54: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:02:54: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Tue, 14 Jul 2020 12:02:54: #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 12:02:54: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:02:54: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:03:04: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:03:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521395/SRX8521395.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:03:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521395/SRX8521395.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:03:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521395/SRX8521395.20_summits.bed INFO @ Tue, 14 Jul 2020 12:03:10: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (81 records, 4 fields): 1 millis CompletedMACS2peakCalling