Job ID = 6627461 SRX = SRX8521387 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T02:37:41 prefetch.2.10.7: 1) Downloading 'SRR11978290'... 2020-07-14T02:37:41 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:39:11 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:39:12 prefetch.2.10.7: 'SRR11978290' is valid 2020-07-14T02:39:12 prefetch.2.10.7: 1) 'SRR11978290' was downloaded successfully 2020-07-14T02:39:12 prefetch.2.10.7: 'SRR11978290' has 0 unresolved dependencies Read 13708696 spots for SRR11978290/SRR11978290.sra Written 13708696 spots for SRR11978290/SRR11978290.sra 2020-07-14T02:40:11 prefetch.2.10.7: 1) Downloading 'SRR11978291'... 2020-07-14T02:40:11 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:42:05 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:42:05 prefetch.2.10.7: 'SRR11978291' is valid 2020-07-14T02:42:05 prefetch.2.10.7: 1) 'SRR11978291' was downloaded successfully 2020-07-14T02:42:05 prefetch.2.10.7: 'SRR11978291' has 0 unresolved dependencies Read 13593007 spots for SRR11978291/SRR11978291.sra Written 13593007 spots for SRR11978291/SRR11978291.sra 2020-07-14T02:43:01 prefetch.2.10.7: 1) Downloading 'SRR11978292'... 2020-07-14T02:43:01 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:44:40 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:44:41 prefetch.2.10.7: 'SRR11978292' is valid 2020-07-14T02:44:41 prefetch.2.10.7: 1) 'SRR11978292' was downloaded successfully 2020-07-14T02:44:41 prefetch.2.10.7: 'SRR11978292' has 0 unresolved dependencies Read 13612443 spots for SRR11978292/SRR11978292.sra Written 13612443 spots for SRR11978292/SRR11978292.sra 2020-07-14T02:45:36 prefetch.2.10.7: 1) Downloading 'SRR11978293'... 2020-07-14T02:45:36 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:47:03 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:47:04 prefetch.2.10.7: 'SRR11978293' is valid 2020-07-14T02:47:04 prefetch.2.10.7: 1) 'SRR11978293' was downloaded successfully 2020-07-14T02:47:04 prefetch.2.10.7: 'SRR11978293' has 0 unresolved dependencies Read 13689254 spots for SRR11978293/SRR11978293.sra Written 13689254 spots for SRR11978293/SRR11978293.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627680 ("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: 00:10:19 54603400 reads; of these: 54603400 (100.00%) were unpaired; of these: 44852977 (82.14%) aligned 0 times 6570258 (12.03%) aligned exactly 1 time 3180165 (5.82%) aligned >1 times 17.86% overall alignment rate Time searching: 00:10:19 Overall time: 00:10:19 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] 2148296 / 9750423 = 0.2203 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 12:01:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521387/SRX8521387.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521387/SRX8521387.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521387/SRX8521387.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521387/SRX8521387.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 12:01:30: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:01:30: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:01:35: 1000000 INFO @ Tue, 14 Jul 2020 12:01:40: 2000000 INFO @ Tue, 14 Jul 2020 12:01:45: 3000000 INFO @ Tue, 14 Jul 2020 12:01:50: 4000000 INFO @ Tue, 14 Jul 2020 12:01:56: 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 12:02:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521387/SRX8521387.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521387/SRX8521387.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521387/SRX8521387.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521387/SRX8521387.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 12:02:00: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:02:00: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:02:01: 6000000 INFO @ Tue, 14 Jul 2020 12:02:05: 1000000 INFO @ Tue, 14 Jul 2020 12:02:07: 7000000 INFO @ Tue, 14 Jul 2020 12:02:10: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 12:02:10: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 12:02:10: #1 total tags in treatment: 7602127 INFO @ Tue, 14 Jul 2020 12:02:10: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:02:10: #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 12:02:10: #1 tags after filtering in treatment: 7602127 INFO @ Tue, 14 Jul 2020 12:02:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:02:10: #1 finished! INFO @ Tue, 14 Jul 2020 12:02:10: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:02:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:02:11: #2 number of paired peaks: 211 WARNING @ Tue, 14 Jul 2020 12:02:11: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Tue, 14 Jul 2020 12:02:11: start model_add_line... INFO @ Tue, 14 Jul 2020 12:02:11: start X-correlation... INFO @ Tue, 14 Jul 2020 12:02:11: end of X-cor INFO @ Tue, 14 Jul 2020 12:02:11: #2 finished! INFO @ Tue, 14 Jul 2020 12:02:11: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 12:02:11: #2 alternative fragment length(s) may be 58 bps INFO @ Tue, 14 Jul 2020 12:02:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521387/SRX8521387.05_model.r WARNING @ Tue, 14 Jul 2020 12:02:11: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:02:11: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Tue, 14 Jul 2020 12:02:11: #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 12:02:11: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:02:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:02:11: 2000000 INFO @ Tue, 14 Jul 2020 12:02:16: 3000000 INFO @ Tue, 14 Jul 2020 12:02:22: 4000000 INFO @ Tue, 14 Jul 2020 12:02:27: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:02:27: 5000000 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 12:02:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521387/SRX8521387.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521387/SRX8521387.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521387/SRX8521387.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521387/SRX8521387.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 12:02:30: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:02:30: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:02:33: 6000000 INFO @ Tue, 14 Jul 2020 12:02:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521387/SRX8521387.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:02:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521387/SRX8521387.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:02:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521387/SRX8521387.05_summits.bed INFO @ Tue, 14 Jul 2020 12:02:34: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1736 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:02:36: 1000000 INFO @ Tue, 14 Jul 2020 12:02:38: 7000000 INFO @ Tue, 14 Jul 2020 12:02:41: 2000000 INFO @ Tue, 14 Jul 2020 12:02:42: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 12:02:42: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 12:02:42: #1 total tags in treatment: 7602127 INFO @ Tue, 14 Jul 2020 12:02:42: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:02:42: #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 12:02:42: #1 tags after filtering in treatment: 7602127 INFO @ Tue, 14 Jul 2020 12:02:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:02:42: #1 finished! INFO @ Tue, 14 Jul 2020 12:02:42: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:02:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:02:42: #2 number of paired peaks: 211 WARNING @ Tue, 14 Jul 2020 12:02:42: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Tue, 14 Jul 2020 12:02:42: start model_add_line... INFO @ Tue, 14 Jul 2020 12:02:42: start X-correlation... INFO @ Tue, 14 Jul 2020 12:02:42: end of X-cor INFO @ Tue, 14 Jul 2020 12:02:42: #2 finished! INFO @ Tue, 14 Jul 2020 12:02:42: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 12:02:42: #2 alternative fragment length(s) may be 58 bps INFO @ Tue, 14 Jul 2020 12:02:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521387/SRX8521387.10_model.r WARNING @ Tue, 14 Jul 2020 12:02:42: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:02:42: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Tue, 14 Jul 2020 12:02:42: #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 12:02:42: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:02:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:02:47: 3000000 INFO @ Tue, 14 Jul 2020 12:02:52: 4000000 INFO @ Tue, 14 Jul 2020 12:02:58: 5000000 INFO @ Tue, 14 Jul 2020 12:02:58: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:03:03: 6000000 INFO @ Tue, 14 Jul 2020 12:03:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521387/SRX8521387.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:03:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521387/SRX8521387.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:03:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521387/SRX8521387.10_summits.bed INFO @ Tue, 14 Jul 2020 12:03:06: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (930 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:03:08: 7000000 INFO @ Tue, 14 Jul 2020 12:03:11: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 12:03:11: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 12:03:11: #1 total tags in treatment: 7602127 INFO @ Tue, 14 Jul 2020 12:03:11: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:03:11: #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 12:03:11: #1 tags after filtering in treatment: 7602127 INFO @ Tue, 14 Jul 2020 12:03:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:03:11: #1 finished! INFO @ Tue, 14 Jul 2020 12:03:11: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:03:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:03:12: #2 number of paired peaks: 211 WARNING @ Tue, 14 Jul 2020 12:03:12: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Tue, 14 Jul 2020 12:03:12: start model_add_line... INFO @ Tue, 14 Jul 2020 12:03:12: start X-correlation... INFO @ Tue, 14 Jul 2020 12:03:12: end of X-cor INFO @ Tue, 14 Jul 2020 12:03:12: #2 finished! INFO @ Tue, 14 Jul 2020 12:03:12: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 12:03:12: #2 alternative fragment length(s) may be 58 bps INFO @ Tue, 14 Jul 2020 12:03:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521387/SRX8521387.20_model.r WARNING @ Tue, 14 Jul 2020 12:03:12: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:03:12: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Tue, 14 Jul 2020 12:03:12: #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 12:03:12: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:03:12: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:03:28: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:03:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521387/SRX8521387.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:03:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521387/SRX8521387.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:03:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521387/SRX8521387.20_summits.bed INFO @ Tue, 14 Jul 2020 12:03:36: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (410 records, 4 fields): 1 millis CompletedMACS2peakCalling