Job ID = 6627281 SRX = SRX8521346 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:49:59 prefetch.2.10.7: 1) Downloading 'SRR11978624'... 2020-07-14T01:49:59 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:51:25 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:51:26 prefetch.2.10.7: 'SRR11978624' is valid 2020-07-14T01:51:26 prefetch.2.10.7: 1) 'SRR11978624' was downloaded successfully 2020-07-14T01:51:26 prefetch.2.10.7: 'SRR11978624' has 0 unresolved dependencies Read 9406722 spots for SRR11978624/SRR11978624.sra Written 9406722 spots for SRR11978624/SRR11978624.sra 2020-07-14T01:52:06 prefetch.2.10.7: 1) Downloading 'SRR11978625'... 2020-07-14T01:52:06 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:53:07 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:53:07 prefetch.2.10.7: 'SRR11978625' is valid 2020-07-14T01:53:07 prefetch.2.10.7: 1) 'SRR11978625' was downloaded successfully 2020-07-14T01:53:07 prefetch.2.10.7: 'SRR11978625' has 0 unresolved dependencies Read 9190342 spots for SRR11978625/SRR11978625.sra Written 9190342 spots for SRR11978625/SRR11978625.sra 2020-07-14T01:53:55 prefetch.2.10.7: 1) Downloading 'SRR11978626'... 2020-07-14T01:53:55 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:55:42 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:55:43 prefetch.2.10.7: 'SRR11978626' is valid 2020-07-14T01:55:43 prefetch.2.10.7: 1) 'SRR11978626' was downloaded successfully 2020-07-14T01:55:43 prefetch.2.10.7: 'SRR11978626' has 0 unresolved dependencies Read 9504008 spots for SRR11978626/SRR11978626.sra Written 9504008 spots for SRR11978626/SRR11978626.sra 2020-07-14T01:56:28 prefetch.2.10.7: 1) Downloading 'SRR11978627'... 2020-07-14T01:56:28 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:57:48 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:57:48 prefetch.2.10.7: 'SRR11978627' is valid 2020-07-14T01:57:48 prefetch.2.10.7: 1) 'SRR11978627' was downloaded successfully 2020-07-14T01:57:48 prefetch.2.10.7: 'SRR11978627' has 0 unresolved dependencies Read 9538237 spots for SRR11978627/SRR11978627.sra Written 9538237 spots for SRR11978627/SRR11978627.sra 2020-07-14T01:58:30 prefetch.2.10.7: 1) Downloading 'SRR11978628'... 2020-07-14T01:58:30 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:58:51 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:58:51 prefetch.2.10.7: 'SRR11978628' is valid 2020-07-14T01:58:51 prefetch.2.10.7: 1) 'SRR11978628' was downloaded successfully 2020-07-14T01:58:51 prefetch.2.10.7: 'SRR11978628' has 0 unresolved dependencies Read 622002 spots for SRR11978628/SRR11978628.sra Written 622002 spots for SRR11978628/SRR11978628.sra 2020-07-14T01:59:08 prefetch.2.10.7: 1) Downloading 'SRR11978629'... 2020-07-14T01:59:08 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:59:27 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:59:27 prefetch.2.10.7: 'SRR11978629' is valid 2020-07-14T01:59:27 prefetch.2.10.7: 1) 'SRR11978629' was downloaded successfully 2020-07-14T01:59:27 prefetch.2.10.7: 'SRR11978629' has 0 unresolved dependencies Read 594868 spots for SRR11978629/SRR11978629.sra Written 594868 spots for SRR11978629/SRR11978629.sra 2020-07-14T01:59:39 prefetch.2.10.7: 1) Downloading 'SRR11978630'... 2020-07-14T01:59:39 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:59:55 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:59:55 prefetch.2.10.7: 'SRR11978630' is valid 2020-07-14T01:59:55 prefetch.2.10.7: 1) 'SRR11978630' was downloaded successfully 2020-07-14T01:59:55 prefetch.2.10.7: 'SRR11978630' has 0 unresolved dependencies Read 632945 spots for SRR11978630/SRR11978630.sra Written 632945 spots for SRR11978630/SRR11978630.sra 2020-07-14T02:00:11 prefetch.2.10.7: 1) Downloading 'SRR11978631'... 2020-07-14T02:00:11 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:00:28 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:00:28 prefetch.2.10.7: 'SRR11978631' is valid 2020-07-14T02:00:28 prefetch.2.10.7: 1) 'SRR11978631' was downloaded successfully 2020-07-14T02:00:28 prefetch.2.10.7: 'SRR11978631' has 0 unresolved dependencies Read 619489 spots for SRR11978631/SRR11978631.sra Written 619489 spots for SRR11978631/SRR11978631.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627517 ("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: 00:06:56 40108613 reads; of these: 40108613 (100.00%) were unpaired; of these: 31573706 (78.72%) aligned 0 times 6675562 (16.64%) aligned exactly 1 time 1859345 (4.64%) aligned >1 times 21.28% overall alignment rate Time searching: 00:06:56 Overall time: 00:06:56 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] 1640931 / 8534907 = 0.1923 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 11:10:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521346/SRX8521346.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521346/SRX8521346.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521346/SRX8521346.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521346/SRX8521346.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 11:10:31: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:10:31: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:10:35: 1000000 INFO @ Tue, 14 Jul 2020 11:10:40: 2000000 INFO @ Tue, 14 Jul 2020 11:10:45: 3000000 INFO @ Tue, 14 Jul 2020 11:10:50: 4000000 INFO @ Tue, 14 Jul 2020 11:10:54: 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 11:10:59: 6000000 INFO @ Tue, 14 Jul 2020 11:11:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521346/SRX8521346.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521346/SRX8521346.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521346/SRX8521346.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521346/SRX8521346.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 11:11:00: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:11:00: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:11:04: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 11:11:04: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 11:11:04: #1 total tags in treatment: 6893976 INFO @ Tue, 14 Jul 2020 11:11:04: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:11:04: #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 11:11:04: #1 tags after filtering in treatment: 6893976 INFO @ Tue, 14 Jul 2020 11:11:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:11:04: #1 finished! INFO @ Tue, 14 Jul 2020 11:11:04: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:11:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:11:04: #2 number of paired peaks: 293 WARNING @ Tue, 14 Jul 2020 11:11:04: Fewer paired peaks (293) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 293 pairs to build model! INFO @ Tue, 14 Jul 2020 11:11:04: start model_add_line... INFO @ Tue, 14 Jul 2020 11:11:04: start X-correlation... INFO @ Tue, 14 Jul 2020 11:11:04: end of X-cor INFO @ Tue, 14 Jul 2020 11:11:04: #2 finished! INFO @ Tue, 14 Jul 2020 11:11:04: #2 predicted fragment length is 62 bps INFO @ Tue, 14 Jul 2020 11:11:04: #2 alternative fragment length(s) may be 49,62,514,547,568,598 bps INFO @ Tue, 14 Jul 2020 11:11:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521346/SRX8521346.05_model.r WARNING @ Tue, 14 Jul 2020 11:11:04: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:11:04: #2 You may need to consider one of the other alternative d(s): 49,62,514,547,568,598 WARNING @ Tue, 14 Jul 2020 11:11:04: #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 11:11:04: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:11:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:11:05: 1000000 INFO @ Tue, 14 Jul 2020 11:11:10: 2000000 INFO @ Tue, 14 Jul 2020 11:11:15: 3000000 INFO @ Tue, 14 Jul 2020 11:11:18: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:11:20: 4000000 INFO @ Tue, 14 Jul 2020 11:11:24: 5000000 INFO @ Tue, 14 Jul 2020 11:11:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521346/SRX8521346.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:11:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521346/SRX8521346.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:11:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521346/SRX8521346.05_summits.bed INFO @ Tue, 14 Jul 2020 11:11:25: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1787 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 11:11:29: 6000000 INFO @ Tue, 14 Jul 2020 11:11:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521346/SRX8521346.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521346/SRX8521346.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521346/SRX8521346.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521346/SRX8521346.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 11:11:30: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:11:30: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:11:34: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 11:11:34: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 11:11:34: #1 total tags in treatment: 6893976 INFO @ Tue, 14 Jul 2020 11:11:34: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:11:34: #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 11:11:34: #1 tags after filtering in treatment: 6893976 INFO @ Tue, 14 Jul 2020 11:11:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:11:34: #1 finished! INFO @ Tue, 14 Jul 2020 11:11:34: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:11:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:11:34: #2 number of paired peaks: 293 WARNING @ Tue, 14 Jul 2020 11:11:34: Fewer paired peaks (293) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 293 pairs to build model! INFO @ Tue, 14 Jul 2020 11:11:34: start model_add_line... INFO @ Tue, 14 Jul 2020 11:11:34: start X-correlation... INFO @ Tue, 14 Jul 2020 11:11:34: end of X-cor INFO @ Tue, 14 Jul 2020 11:11:34: #2 finished! INFO @ Tue, 14 Jul 2020 11:11:34: #2 predicted fragment length is 62 bps INFO @ Tue, 14 Jul 2020 11:11:34: #2 alternative fragment length(s) may be 49,62,514,547,568,598 bps INFO @ Tue, 14 Jul 2020 11:11:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521346/SRX8521346.10_model.r WARNING @ Tue, 14 Jul 2020 11:11:34: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:11:34: #2 You may need to consider one of the other alternative d(s): 49,62,514,547,568,598 WARNING @ Tue, 14 Jul 2020 11:11:34: #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 11:11:34: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:11:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:11:36: 1000000 INFO @ Tue, 14 Jul 2020 11:11:41: 2000000 INFO @ Tue, 14 Jul 2020 11:11:46: 3000000 INFO @ Tue, 14 Jul 2020 11:11:48: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:11:51: 4000000 INFO @ Tue, 14 Jul 2020 11:11:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521346/SRX8521346.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:11:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521346/SRX8521346.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:11:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521346/SRX8521346.10_summits.bed INFO @ Tue, 14 Jul 2020 11:11:55: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (723 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:11:56: 5000000 INFO @ Tue, 14 Jul 2020 11:12:01: 6000000 INFO @ Tue, 14 Jul 2020 11:12:05: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 11:12:05: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 11:12:05: #1 total tags in treatment: 6893976 INFO @ Tue, 14 Jul 2020 11:12:05: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:12:05: #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 11:12:05: #1 tags after filtering in treatment: 6893976 INFO @ Tue, 14 Jul 2020 11:12:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:12:05: #1 finished! INFO @ Tue, 14 Jul 2020 11:12:05: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:12:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:12:06: #2 number of paired peaks: 293 WARNING @ Tue, 14 Jul 2020 11:12:06: Fewer paired peaks (293) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 293 pairs to build model! INFO @ Tue, 14 Jul 2020 11:12:06: start model_add_line... INFO @ Tue, 14 Jul 2020 11:12:06: start X-correlation... INFO @ Tue, 14 Jul 2020 11:12:06: end of X-cor INFO @ Tue, 14 Jul 2020 11:12:06: #2 finished! INFO @ Tue, 14 Jul 2020 11:12:06: #2 predicted fragment length is 62 bps INFO @ Tue, 14 Jul 2020 11:12:06: #2 alternative fragment length(s) may be 49,62,514,547,568,598 bps INFO @ Tue, 14 Jul 2020 11:12:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521346/SRX8521346.20_model.r WARNING @ Tue, 14 Jul 2020 11:12:06: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:12:06: #2 You may need to consider one of the other alternative d(s): 49,62,514,547,568,598 WARNING @ Tue, 14 Jul 2020 11:12:06: #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 11:12:06: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:12:06: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:12:20: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:12:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521346/SRX8521346.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:12:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521346/SRX8521346.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:12:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521346/SRX8521346.20_summits.bed INFO @ Tue, 14 Jul 2020 11:12:28: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (147 records, 4 fields): 1 millis CompletedMACS2peakCalling