Job ID = 6627112 SRX = SRX8521290 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T00:57:02 prefetch.2.10.7: 1) Downloading 'SRR11978450'... 2020-07-14T00:57:02 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T00:57:44 prefetch.2.10.7: HTTPS download succeed 2020-07-14T00:57:44 prefetch.2.10.7: 'SRR11978450' is valid 2020-07-14T00:57:44 prefetch.2.10.7: 1) 'SRR11978450' was downloaded successfully 2020-07-14T00:57:44 prefetch.2.10.7: 'SRR11978450' has 0 unresolved dependencies Read 4599048 spots for SRR11978450/SRR11978450.sra Written 4599048 spots for SRR11978450/SRR11978450.sra 2020-07-14T00:58:23 prefetch.2.10.7: 1) Downloading 'SRR11978451'... 2020-07-14T00:58:23 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T00:59:12 prefetch.2.10.7: HTTPS download succeed 2020-07-14T00:59:12 prefetch.2.10.7: 'SRR11978451' is valid 2020-07-14T00:59:12 prefetch.2.10.7: 1) 'SRR11978451' was downloaded successfully 2020-07-14T00:59:12 prefetch.2.10.7: 'SRR11978451' has 0 unresolved dependencies Read 4547063 spots for SRR11978451/SRR11978451.sra Written 4547063 spots for SRR11978451/SRR11978451.sra 2020-07-14T00:59:40 prefetch.2.10.7: 1) Downloading 'SRR11978452'... 2020-07-14T00:59:40 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:00:55 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:00:56 prefetch.2.10.7: 'SRR11978452' is valid 2020-07-14T01:00:56 prefetch.2.10.7: 1) 'SRR11978452' was downloaded successfully 2020-07-14T01:00:56 prefetch.2.10.7: 'SRR11978452' has 0 unresolved dependencies Read 4688556 spots for SRR11978452/SRR11978452.sra Written 4688556 spots for SRR11978452/SRR11978452.sra 2020-07-14T01:01:23 prefetch.2.10.7: 1) Downloading 'SRR11978453'... 2020-07-14T01:01:23 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:02:44 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:02:44 prefetch.2.10.7: 'SRR11978453' is valid 2020-07-14T01:02:44 prefetch.2.10.7: 1) 'SRR11978453' was downloaded successfully 2020-07-14T01:02:44 prefetch.2.10.7: 'SRR11978453' has 0 unresolved dependencies Read 4644414 spots for SRR11978453/SRR11978453.sra Written 4644414 spots for SRR11978453/SRR11978453.sra 2020-07-14T01:03:13 prefetch.2.10.7: 1) Downloading 'SRR11978454'... 2020-07-14T01:03:13 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:03:57 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:03:57 prefetch.2.10.7: 'SRR11978454' is valid 2020-07-14T01:03:57 prefetch.2.10.7: 1) 'SRR11978454' was downloaded successfully 2020-07-14T01:03:57 prefetch.2.10.7: 'SRR11978454' has 0 unresolved dependencies Read 5521400 spots for SRR11978454/SRR11978454.sra Written 5521400 spots for SRR11978454/SRR11978454.sra 2020-07-14T01:04:37 prefetch.2.10.7: 1) Downloading 'SRR11978455'... 2020-07-14T01:04:37 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:05:49 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:05:49 prefetch.2.10.7: 'SRR11978455' is valid 2020-07-14T01:05:49 prefetch.2.10.7: 1) 'SRR11978455' was downloaded successfully 2020-07-14T01:05:49 prefetch.2.10.7: 'SRR11978455' has 0 unresolved dependencies Read 5285653 spots for SRR11978455/SRR11978455.sra Written 5285653 spots for SRR11978455/SRR11978455.sra 2020-07-14T01:06:20 prefetch.2.10.7: 1) Downloading 'SRR11978456'... 2020-07-14T01:06:20 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:08:38 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:08:38 prefetch.2.10.7: 'SRR11978456' is valid 2020-07-14T01:08:38 prefetch.2.10.7: 1) 'SRR11978456' was downloaded successfully 2020-07-14T01:08:38 prefetch.2.10.7: 'SRR11978456' has 0 unresolved dependencies Read 5615508 spots for SRR11978456/SRR11978456.sra Written 5615508 spots for SRR11978456/SRR11978456.sra 2020-07-14T01:09:09 prefetch.2.10.7: 1) Downloading 'SRR11978457'... 2020-07-14T01:09:09 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:10:23 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:10:24 prefetch.2.10.7: 'SRR11978457' is valid 2020-07-14T01:10:24 prefetch.2.10.7: 1) 'SRR11978457' was downloaded successfully 2020-07-14T01:10:24 prefetch.2.10.7: 'SRR11978457' has 0 unresolved dependencies Read 5504412 spots for SRR11978457/SRR11978457.sra Written 5504412 spots for SRR11978457/SRR11978457.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627353 ("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: 00:06:55 40406054 reads; of these: 40406054 (100.00%) were unpaired; of these: 34270239 (84.81%) aligned 0 times 4711353 (11.66%) aligned exactly 1 time 1424462 (3.53%) aligned >1 times 15.19% overall alignment rate Time searching: 00:06:55 Overall time: 00:06:55 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] 1205363 / 6135815 = 0.1964 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 10:20:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521290/SRX8521290.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521290/SRX8521290.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521290/SRX8521290.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521290/SRX8521290.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 10:20:24: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:20:24: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:20:31: 1000000 INFO @ Tue, 14 Jul 2020 10:20:36: 2000000 INFO @ Tue, 14 Jul 2020 10:20:42: 3000000 INFO @ Tue, 14 Jul 2020 10:20:48: 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 10:20:53: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 10:20:53: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 10:20:53: #1 total tags in treatment: 4930452 INFO @ Tue, 14 Jul 2020 10:20:53: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:20:53: #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 10:20:53: #1 tags after filtering in treatment: 4930452 INFO @ Tue, 14 Jul 2020 10:20:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:20:53: #1 finished! INFO @ Tue, 14 Jul 2020 10:20:53: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:20:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:20:54: #2 number of paired peaks: 577 WARNING @ Tue, 14 Jul 2020 10:20:54: Fewer paired peaks (577) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 577 pairs to build model! INFO @ Tue, 14 Jul 2020 10:20:54: start model_add_line... INFO @ Tue, 14 Jul 2020 10:20:54: start X-correlation... INFO @ Tue, 14 Jul 2020 10:20:54: end of X-cor INFO @ Tue, 14 Jul 2020 10:20:54: #2 finished! INFO @ Tue, 14 Jul 2020 10:20:54: #2 predicted fragment length is 66 bps INFO @ Tue, 14 Jul 2020 10:20:54: #2 alternative fragment length(s) may be 66 bps INFO @ Tue, 14 Jul 2020 10:20:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521290/SRX8521290.05_model.r WARNING @ Tue, 14 Jul 2020 10:20:54: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:20:54: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Tue, 14 Jul 2020 10:20:54: #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 10:20:54: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:20:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:20:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521290/SRX8521290.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521290/SRX8521290.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521290/SRX8521290.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521290/SRX8521290.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 10:20:54: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:20:54: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:21:00: 1000000 INFO @ Tue, 14 Jul 2020 10:21:06: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:21:06: 2000000 INFO @ Tue, 14 Jul 2020 10:21:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521290/SRX8521290.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:21:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521290/SRX8521290.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:21:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521290/SRX8521290.05_summits.bed INFO @ Tue, 14 Jul 2020 10:21:12: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2469 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:21:12: 3000000 INFO @ Tue, 14 Jul 2020 10:21:18: 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 10:21:23: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 10:21:23: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 10:21:23: #1 total tags in treatment: 4930452 INFO @ Tue, 14 Jul 2020 10:21:23: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:21:23: #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 10:21:23: #1 tags after filtering in treatment: 4930452 INFO @ Tue, 14 Jul 2020 10:21:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:21:23: #1 finished! INFO @ Tue, 14 Jul 2020 10:21:23: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:21:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:21:24: #2 number of paired peaks: 577 WARNING @ Tue, 14 Jul 2020 10:21:24: Fewer paired peaks (577) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 577 pairs to build model! INFO @ Tue, 14 Jul 2020 10:21:24: start model_add_line... INFO @ Tue, 14 Jul 2020 10:21:24: start X-correlation... INFO @ Tue, 14 Jul 2020 10:21:24: end of X-cor INFO @ Tue, 14 Jul 2020 10:21:24: #2 finished! INFO @ Tue, 14 Jul 2020 10:21:24: #2 predicted fragment length is 66 bps INFO @ Tue, 14 Jul 2020 10:21:24: #2 alternative fragment length(s) may be 66 bps INFO @ Tue, 14 Jul 2020 10:21:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521290/SRX8521290.10_model.r WARNING @ Tue, 14 Jul 2020 10:21:24: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:21:24: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Tue, 14 Jul 2020 10:21:24: #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 10:21:24: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:21:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:21:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521290/SRX8521290.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521290/SRX8521290.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521290/SRX8521290.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521290/SRX8521290.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 10:21:24: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:21:24: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:21:30: 1000000 INFO @ Tue, 14 Jul 2020 10:21:35: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:21:36: 2000000 INFO @ Tue, 14 Jul 2020 10:21:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521290/SRX8521290.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:21:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521290/SRX8521290.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:21:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521290/SRX8521290.10_summits.bed INFO @ Tue, 14 Jul 2020 10:21:41: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (855 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:21:42: 3000000 INFO @ Tue, 14 Jul 2020 10:21:48: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:21:53: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 10:21:53: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 10:21:53: #1 total tags in treatment: 4930452 INFO @ Tue, 14 Jul 2020 10:21:53: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:21:53: #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 10:21:53: #1 tags after filtering in treatment: 4930452 INFO @ Tue, 14 Jul 2020 10:21:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:21:53: #1 finished! INFO @ Tue, 14 Jul 2020 10:21:53: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:21:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:21:54: #2 number of paired peaks: 577 WARNING @ Tue, 14 Jul 2020 10:21:54: Fewer paired peaks (577) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 577 pairs to build model! INFO @ Tue, 14 Jul 2020 10:21:54: start model_add_line... INFO @ Tue, 14 Jul 2020 10:21:54: start X-correlation... INFO @ Tue, 14 Jul 2020 10:21:54: end of X-cor INFO @ Tue, 14 Jul 2020 10:21:54: #2 finished! INFO @ Tue, 14 Jul 2020 10:21:54: #2 predicted fragment length is 66 bps INFO @ Tue, 14 Jul 2020 10:21:54: #2 alternative fragment length(s) may be 66 bps INFO @ Tue, 14 Jul 2020 10:21:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521290/SRX8521290.20_model.r WARNING @ Tue, 14 Jul 2020 10:21:54: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:21:54: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Tue, 14 Jul 2020 10:21:54: #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 10:21:54: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:21:54: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:22:05: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:22:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521290/SRX8521290.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:22:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521290/SRX8521290.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:22:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521290/SRX8521290.20_summits.bed INFO @ Tue, 14 Jul 2020 10:22:11: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (211 records, 4 fields): 2 millis CompletedMACS2peakCalling