Job ID = 6627577 SRX = SRX8521411 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T03:03:48 prefetch.2.10.7: 1) Downloading 'SRR11978386'... 2020-07-14T03:03:48 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:05:24 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:05:24 prefetch.2.10.7: 'SRR11978386' is valid 2020-07-14T03:05:24 prefetch.2.10.7: 1) 'SRR11978386' was downloaded successfully 2020-07-14T03:05:24 prefetch.2.10.7: 'SRR11978386' has 0 unresolved dependencies Read 12235709 spots for SRR11978386/SRR11978386.sra Written 12235709 spots for SRR11978386/SRR11978386.sra 2020-07-14T03:06:35 prefetch.2.10.7: 1) Downloading 'SRR11978387'... 2020-07-14T03:06:35 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:07:53 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:07:53 prefetch.2.10.7: 'SRR11978387' is valid 2020-07-14T03:07:53 prefetch.2.10.7: 1) 'SRR11978387' was downloaded successfully 2020-07-14T03:07:53 prefetch.2.10.7: 'SRR11978387' has 0 unresolved dependencies Read 11651097 spots for SRR11978387/SRR11978387.sra Written 11651097 spots for SRR11978387/SRR11978387.sra 2020-07-14T03:09:02 prefetch.2.10.7: 1) Downloading 'SRR11978388'... 2020-07-14T03:09:02 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:10:05 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:10:05 prefetch.2.10.7: 'SRR11978388' is valid 2020-07-14T03:10:05 prefetch.2.10.7: 1) 'SRR11978388' was downloaded successfully 2020-07-14T03:10:05 prefetch.2.10.7: 'SRR11978388' has 0 unresolved dependencies Read 11513229 spots for SRR11978388/SRR11978388.sra Written 11513229 spots for SRR11978388/SRR11978388.sra 2020-07-14T03:10:54 prefetch.2.10.7: 1) Downloading 'SRR11978389'... 2020-07-14T03:10:54 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:12:04 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:12:04 prefetch.2.10.7: 'SRR11978389' is valid 2020-07-14T03:12:04 prefetch.2.10.7: 1) 'SRR11978389' was downloaded successfully 2020-07-14T03:12:04 prefetch.2.10.7: 'SRR11978389' has 0 unresolved dependencies Read 11562098 spots for SRR11978389/SRR11978389.sra Written 11562098 spots for SRR11978389/SRR11978389.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627770 ("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: 00:08:55 46962133 reads; of these: 46962133 (100.00%) were unpaired; of these: 35584720 (75.77%) aligned 0 times 7920310 (16.87%) aligned exactly 1 time 3457103 (7.36%) aligned >1 times 24.23% overall alignment rate Time searching: 00:08:55 Overall time: 00:08:55 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_sort_core] merging from 8 files... [bam_rmdupse_core] 1992907 / 11377413 = 0.1752 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 12:25:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521411/SRX8521411.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521411/SRX8521411.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521411/SRX8521411.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521411/SRX8521411.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 12:25:32: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:25:32: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:25:39: 1000000 INFO @ Tue, 14 Jul 2020 12:25:45: 2000000 INFO @ Tue, 14 Jul 2020 12:25:52: 3000000 INFO @ Tue, 14 Jul 2020 12:26:00: 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 12:26:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521411/SRX8521411.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521411/SRX8521411.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521411/SRX8521411.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521411/SRX8521411.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 12:26:02: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:26:02: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:26:08: 5000000 INFO @ Tue, 14 Jul 2020 12:26:09: 1000000 INFO @ Tue, 14 Jul 2020 12:26:15: 6000000 INFO @ Tue, 14 Jul 2020 12:26:15: 2000000 INFO @ Tue, 14 Jul 2020 12:26:22: 3000000 INFO @ Tue, 14 Jul 2020 12:26:23: 7000000 INFO @ Tue, 14 Jul 2020 12:26:29: 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 12:26:31: 8000000 INFO @ Tue, 14 Jul 2020 12:26:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521411/SRX8521411.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521411/SRX8521411.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521411/SRX8521411.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521411/SRX8521411.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 12:26:32: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:26:32: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:26:36: 5000000 INFO @ Tue, 14 Jul 2020 12:26:39: 9000000 INFO @ Tue, 14 Jul 2020 12:26:39: 1000000 INFO @ Tue, 14 Jul 2020 12:26:42: #1 tag size is determined as 58 bps INFO @ Tue, 14 Jul 2020 12:26:42: #1 tag size = 58 INFO @ Tue, 14 Jul 2020 12:26:42: #1 total tags in treatment: 9384506 INFO @ Tue, 14 Jul 2020 12:26:42: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:26:42: #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 12:26:42: #1 tags after filtering in treatment: 9384506 INFO @ Tue, 14 Jul 2020 12:26:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:26:42: #1 finished! INFO @ Tue, 14 Jul 2020 12:26:42: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:26:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:26:42: #2 number of paired peaks: 133 WARNING @ Tue, 14 Jul 2020 12:26:42: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Tue, 14 Jul 2020 12:26:42: start model_add_line... INFO @ Tue, 14 Jul 2020 12:26:42: start X-correlation... INFO @ Tue, 14 Jul 2020 12:26:42: end of X-cor INFO @ Tue, 14 Jul 2020 12:26:42: #2 finished! INFO @ Tue, 14 Jul 2020 12:26:42: #2 predicted fragment length is 50 bps INFO @ Tue, 14 Jul 2020 12:26:42: #2 alternative fragment length(s) may be 50 bps INFO @ Tue, 14 Jul 2020 12:26:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521411/SRX8521411.05_model.r WARNING @ Tue, 14 Jul 2020 12:26:42: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:26:42: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Tue, 14 Jul 2020 12:26:42: #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 12:26:42: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:26:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:26:43: 6000000 INFO @ Tue, 14 Jul 2020 12:26:46: 2000000 INFO @ Tue, 14 Jul 2020 12:26:50: 7000000 INFO @ Tue, 14 Jul 2020 12:26:53: 3000000 INFO @ Tue, 14 Jul 2020 12:26:57: 8000000 INFO @ Tue, 14 Jul 2020 12:27:00: 4000000 INFO @ Tue, 14 Jul 2020 12:27:01: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:27:03: 9000000 INFO @ Tue, 14 Jul 2020 12:27:06: #1 tag size is determined as 58 bps INFO @ Tue, 14 Jul 2020 12:27:06: #1 tag size = 58 INFO @ Tue, 14 Jul 2020 12:27:06: #1 total tags in treatment: 9384506 INFO @ Tue, 14 Jul 2020 12:27:06: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:27:06: #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 12:27:06: #1 tags after filtering in treatment: 9384506 INFO @ Tue, 14 Jul 2020 12:27:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:27:06: #1 finished! INFO @ Tue, 14 Jul 2020 12:27:06: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:27:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:27:06: 5000000 INFO @ Tue, 14 Jul 2020 12:27:07: #2 number of paired peaks: 133 WARNING @ Tue, 14 Jul 2020 12:27:07: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Tue, 14 Jul 2020 12:27:07: start model_add_line... INFO @ Tue, 14 Jul 2020 12:27:07: start X-correlation... INFO @ Tue, 14 Jul 2020 12:27:07: end of X-cor INFO @ Tue, 14 Jul 2020 12:27:07: #2 finished! INFO @ Tue, 14 Jul 2020 12:27:07: #2 predicted fragment length is 50 bps INFO @ Tue, 14 Jul 2020 12:27:07: #2 alternative fragment length(s) may be 50 bps INFO @ Tue, 14 Jul 2020 12:27:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521411/SRX8521411.10_model.r WARNING @ Tue, 14 Jul 2020 12:27:07: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:27:07: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Tue, 14 Jul 2020 12:27:07: #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 12:27:07: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:27:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:27:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521411/SRX8521411.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:27:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521411/SRX8521411.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:27:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521411/SRX8521411.05_summits.bed INFO @ Tue, 14 Jul 2020 12:27:11: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1590 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:27:13: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:27:19: 7000000 INFO @ Tue, 14 Jul 2020 12:27:25: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:27:25: 8000000 INFO @ Tue, 14 Jul 2020 12:27:32: 9000000 INFO @ Tue, 14 Jul 2020 12:27:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521411/SRX8521411.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:27:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521411/SRX8521411.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:27:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521411/SRX8521411.10_summits.bed INFO @ Tue, 14 Jul 2020 12:27:34: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (753 records, 4 fields): 2 millis INFO @ Tue, 14 Jul 2020 12:27:34: #1 tag size is determined as 58 bps INFO @ Tue, 14 Jul 2020 12:27:34: #1 tag size = 58 INFO @ Tue, 14 Jul 2020 12:27:34: #1 total tags in treatment: 9384506 INFO @ Tue, 14 Jul 2020 12:27:34: #1 user defined the maximum tags... CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:27:34: #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 12:27:34: #1 tags after filtering in treatment: 9384506 INFO @ Tue, 14 Jul 2020 12:27:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:27:34: #1 finished! INFO @ Tue, 14 Jul 2020 12:27:34: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:27:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:27:35: #2 number of paired peaks: 133 WARNING @ Tue, 14 Jul 2020 12:27:35: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Tue, 14 Jul 2020 12:27:35: start model_add_line... INFO @ Tue, 14 Jul 2020 12:27:35: start X-correlation... INFO @ Tue, 14 Jul 2020 12:27:35: end of X-cor INFO @ Tue, 14 Jul 2020 12:27:35: #2 finished! INFO @ Tue, 14 Jul 2020 12:27:35: #2 predicted fragment length is 50 bps INFO @ Tue, 14 Jul 2020 12:27:35: #2 alternative fragment length(s) may be 50 bps INFO @ Tue, 14 Jul 2020 12:27:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521411/SRX8521411.20_model.r WARNING @ Tue, 14 Jul 2020 12:27:35: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:27:35: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Tue, 14 Jul 2020 12:27:35: #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 12:27:35: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:27:35: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:27:53: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:28:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521411/SRX8521411.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:28:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521411/SRX8521411.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:28:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521411/SRX8521411.20_summits.bed INFO @ Tue, 14 Jul 2020 12:28:02: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (322 records, 4 fields): 2 millis CompletedMACS2peakCalling