Job ID = 6454346 SRX = SRX201883 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:23:29 prefetch.2.10.7: 1) Downloading 'SRR609673'... 2020-06-21T09:23:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:41:16 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:41:16 prefetch.2.10.7: 1) 'SRR609673' was downloaded successfully Read 46632369 spots for SRR609673/SRR609673.sra Written 46632369 spots for SRR609673/SRR609673.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:34:11 46632369 reads; of these: 46632369 (100.00%) were unpaired; of these: 1795763 (3.85%) aligned 0 times 13134948 (28.17%) aligned exactly 1 time 31701658 (67.98%) aligned >1 times 96.15% overall alignment rate Time searching: 00:34:11 Overall time: 00:34:11 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 23178793 / 44836606 = 0.5170 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 @ Sun, 21 Jun 2020 19:32:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX201883/SRX201883.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX201883/SRX201883.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX201883/SRX201883.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX201883/SRX201883.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 @ Sun, 21 Jun 2020 19:32:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:32:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:32:23: 1000000 INFO @ Sun, 21 Jun 2020 19:32:29: 2000000 INFO @ Sun, 21 Jun 2020 19:32:35: 3000000 INFO @ Sun, 21 Jun 2020 19:32:41: 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 @ Sun, 21 Jun 2020 19:32:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX201883/SRX201883.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX201883/SRX201883.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX201883/SRX201883.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX201883/SRX201883.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 @ Sun, 21 Jun 2020 19:32:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:32:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:32:47: 5000000 INFO @ Sun, 21 Jun 2020 19:32:54: 6000000 INFO @ Sun, 21 Jun 2020 19:32:54: 1000000 INFO @ Sun, 21 Jun 2020 19:33:00: 2000000 INFO @ Sun, 21 Jun 2020 19:33:00: 7000000 INFO @ Sun, 21 Jun 2020 19:33:06: 3000000 INFO @ Sun, 21 Jun 2020 19:33:06: 8000000 INFO @ Sun, 21 Jun 2020 19:33:12: 4000000 INFO @ Sun, 21 Jun 2020 19:33:12: 9000000 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 @ Sun, 21 Jun 2020 19:33:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX201883/SRX201883.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX201883/SRX201883.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX201883/SRX201883.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX201883/SRX201883.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 @ Sun, 21 Jun 2020 19:33:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:33:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:33:19: 5000000 INFO @ Sun, 21 Jun 2020 19:33:19: 10000000 INFO @ Sun, 21 Jun 2020 19:33:25: 1000000 INFO @ Sun, 21 Jun 2020 19:33:25: 11000000 INFO @ Sun, 21 Jun 2020 19:33:25: 6000000 INFO @ Sun, 21 Jun 2020 19:33:32: 12000000 INFO @ Sun, 21 Jun 2020 19:33:32: 7000000 INFO @ Sun, 21 Jun 2020 19:33:32: 2000000 INFO @ Sun, 21 Jun 2020 19:33:38: 13000000 INFO @ Sun, 21 Jun 2020 19:33:38: 8000000 INFO @ Sun, 21 Jun 2020 19:33:40: 3000000 INFO @ Sun, 21 Jun 2020 19:33:44: 14000000 INFO @ Sun, 21 Jun 2020 19:33:45: 9000000 INFO @ Sun, 21 Jun 2020 19:33:47: 4000000 INFO @ Sun, 21 Jun 2020 19:33:51: 15000000 INFO @ Sun, 21 Jun 2020 19:33:51: 10000000 INFO @ Sun, 21 Jun 2020 19:33:55: 5000000 INFO @ Sun, 21 Jun 2020 19:33:57: 16000000 INFO @ Sun, 21 Jun 2020 19:33:58: 11000000 INFO @ Sun, 21 Jun 2020 19:34:02: 6000000 INFO @ Sun, 21 Jun 2020 19:34:04: 17000000 INFO @ Sun, 21 Jun 2020 19:34:04: 12000000 INFO @ Sun, 21 Jun 2020 19:34:10: 7000000 INFO @ Sun, 21 Jun 2020 19:34:10: 18000000 INFO @ Sun, 21 Jun 2020 19:34:10: 13000000 INFO @ Sun, 21 Jun 2020 19:34:17: 14000000 INFO @ Sun, 21 Jun 2020 19:34:17: 19000000 INFO @ Sun, 21 Jun 2020 19:34:17: 8000000 INFO @ Sun, 21 Jun 2020 19:34:23: 20000000 INFO @ Sun, 21 Jun 2020 19:34:23: 15000000 INFO @ Sun, 21 Jun 2020 19:34:25: 9000000 INFO @ Sun, 21 Jun 2020 19:34:30: 21000000 INFO @ Sun, 21 Jun 2020 19:34:30: 16000000 INFO @ Sun, 21 Jun 2020 19:34:32: 10000000 INFO @ Sun, 21 Jun 2020 19:34:34: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 19:34:34: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 19:34:34: #1 total tags in treatment: 21657813 INFO @ Sun, 21 Jun 2020 19:34:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:34:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:34:35: #1 tags after filtering in treatment: 21657733 INFO @ Sun, 21 Jun 2020 19:34:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:34:35: #1 finished! INFO @ Sun, 21 Jun 2020 19:34:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:34:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:34:36: 17000000 INFO @ Sun, 21 Jun 2020 19:34:37: #2 number of paired peaks: 9958 INFO @ Sun, 21 Jun 2020 19:34:37: start model_add_line... INFO @ Sun, 21 Jun 2020 19:34:37: start X-correlation... INFO @ Sun, 21 Jun 2020 19:34:37: end of X-cor INFO @ Sun, 21 Jun 2020 19:34:37: #2 finished! INFO @ Sun, 21 Jun 2020 19:34:37: #2 predicted fragment length is 145 bps INFO @ Sun, 21 Jun 2020 19:34:37: #2 alternative fragment length(s) may be 3,145 bps INFO @ Sun, 21 Jun 2020 19:34:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX201883/SRX201883.05_model.r WARNING @ Sun, 21 Jun 2020 19:34:37: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:34:37: #2 You may need to consider one of the other alternative d(s): 3,145 WARNING @ Sun, 21 Jun 2020 19:34:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:34:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:34:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:34:39: 11000000 INFO @ Sun, 21 Jun 2020 19:34:42: 18000000 INFO @ Sun, 21 Jun 2020 19:34:47: 12000000 INFO @ Sun, 21 Jun 2020 19:34:49: 19000000 INFO @ Sun, 21 Jun 2020 19:34:54: 13000000 INFO @ Sun, 21 Jun 2020 19:34:55: 20000000 INFO @ Sun, 21 Jun 2020 19:35:01: 14000000 INFO @ Sun, 21 Jun 2020 19:35:02: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:35:06: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 19:35:06: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 19:35:06: #1 total tags in treatment: 21657813 INFO @ Sun, 21 Jun 2020 19:35:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:35:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:35:07: #1 tags after filtering in treatment: 21657733 INFO @ Sun, 21 Jun 2020 19:35:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:35:07: #1 finished! INFO @ Sun, 21 Jun 2020 19:35:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:35:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:35:08: 15000000 INFO @ Sun, 21 Jun 2020 19:35:09: #2 number of paired peaks: 9958 INFO @ Sun, 21 Jun 2020 19:35:09: start model_add_line... INFO @ Sun, 21 Jun 2020 19:35:09: start X-correlation... INFO @ Sun, 21 Jun 2020 19:35:09: end of X-cor INFO @ Sun, 21 Jun 2020 19:35:09: #2 finished! INFO @ Sun, 21 Jun 2020 19:35:09: #2 predicted fragment length is 145 bps INFO @ Sun, 21 Jun 2020 19:35:09: #2 alternative fragment length(s) may be 3,145 bps INFO @ Sun, 21 Jun 2020 19:35:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX201883/SRX201883.10_model.r WARNING @ Sun, 21 Jun 2020 19:35:09: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:35:09: #2 You may need to consider one of the other alternative d(s): 3,145 WARNING @ Sun, 21 Jun 2020 19:35:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:35:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:35:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:35:15: 16000000 INFO @ Sun, 21 Jun 2020 19:35:23: 17000000 INFO @ Sun, 21 Jun 2020 19:35:30: 18000000 INFO @ Sun, 21 Jun 2020 19:35:31: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:35:37: 19000000 INFO @ Sun, 21 Jun 2020 19:35:44: 20000000 INFO @ Sun, 21 Jun 2020 19:35:51: 21000000 INFO @ Sun, 21 Jun 2020 19:35:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX201883/SRX201883.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:35:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX201883/SRX201883.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:35:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX201883/SRX201883.05_summits.bed INFO @ Sun, 21 Jun 2020 19:35:52: Done! pass1 - making usageList (1094 chroms): 4 millis pass2 - checking and writing primary data (14666 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:35:56: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 19:35:56: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 19:35:56: #1 total tags in treatment: 21657813 INFO @ Sun, 21 Jun 2020 19:35:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:35:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:35:56: #1 tags after filtering in treatment: 21657733 INFO @ Sun, 21 Jun 2020 19:35:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:35:56: #1 finished! INFO @ Sun, 21 Jun 2020 19:35:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:35:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:35:59: #2 number of paired peaks: 9958 INFO @ Sun, 21 Jun 2020 19:35:59: start model_add_line... INFO @ Sun, 21 Jun 2020 19:35:59: start X-correlation... INFO @ Sun, 21 Jun 2020 19:35:59: end of X-cor INFO @ Sun, 21 Jun 2020 19:35:59: #2 finished! INFO @ Sun, 21 Jun 2020 19:35:59: #2 predicted fragment length is 145 bps INFO @ Sun, 21 Jun 2020 19:35:59: #2 alternative fragment length(s) may be 3,145 bps INFO @ Sun, 21 Jun 2020 19:35:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX201883/SRX201883.20_model.r WARNING @ Sun, 21 Jun 2020 19:35:59: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:35:59: #2 You may need to consider one of the other alternative d(s): 3,145 WARNING @ Sun, 21 Jun 2020 19:35:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:35:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:35:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:36:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:36:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX201883/SRX201883.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:36:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX201883/SRX201883.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:36:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX201883/SRX201883.10_summits.bed INFO @ Sun, 21 Jun 2020 19:36:21: Done! pass1 - making usageList (1027 chroms): 3 millis pass2 - checking and writing primary data (10277 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:36:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:37:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX201883/SRX201883.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:37:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX201883/SRX201883.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:37:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX201883/SRX201883.20_summits.bed INFO @ Sun, 21 Jun 2020 19:37:10: Done! pass1 - making usageList (918 chroms): 1 millis pass2 - checking and writing primary data (5649 records, 4 fields): 27 millis CompletedMACS2peakCalling