Job ID = 6453677 SRX = SRX1361346 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:32:11 prefetch.2.10.7: 1) Downloading 'SRR2749784'... 2020-06-21T08:32:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:41:27 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:41:27 prefetch.2.10.7: 1) 'SRR2749784' was downloaded successfully Read 59592662 spots for SRR2749784/SRR2749784.sra Written 59592662 spots for SRR2749784/SRR2749784.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:20:15 59592662 reads; of these: 59592662 (100.00%) were unpaired; of these: 1953165 (3.28%) aligned 0 times 26902858 (45.14%) aligned exactly 1 time 30736639 (51.58%) aligned >1 times 96.72% overall alignment rate Time searching: 00:20:16 Overall time: 00:20:16 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 24 files... [bam_rmdupse_core] 30962047 / 57639497 = 0.5372 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 18:17:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1361346/SRX1361346.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1361346/SRX1361346.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1361346/SRX1361346.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1361346/SRX1361346.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 18:17:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:17:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:17:38: 1000000 INFO @ Sun, 21 Jun 2020 18:17:44: 2000000 INFO @ Sun, 21 Jun 2020 18:17:49: 3000000 INFO @ Sun, 21 Jun 2020 18:17:54: 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 18:17:59: 5000000 INFO @ Sun, 21 Jun 2020 18:18:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1361346/SRX1361346.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1361346/SRX1361346.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1361346/SRX1361346.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1361346/SRX1361346.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 18:18:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:18:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:18:04: 6000000 INFO @ Sun, 21 Jun 2020 18:18:07: 1000000 INFO @ Sun, 21 Jun 2020 18:18:09: 7000000 INFO @ Sun, 21 Jun 2020 18:18:13: 2000000 INFO @ Sun, 21 Jun 2020 18:18:15: 8000000 INFO @ Sun, 21 Jun 2020 18:18:18: 3000000 INFO @ Sun, 21 Jun 2020 18:18:20: 9000000 INFO @ Sun, 21 Jun 2020 18:18:23: 4000000 INFO @ Sun, 21 Jun 2020 18:18:25: 10000000 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 18:18:29: 5000000 INFO @ Sun, 21 Jun 2020 18:18:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1361346/SRX1361346.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1361346/SRX1361346.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1361346/SRX1361346.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1361346/SRX1361346.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 18:18:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:18:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:18:31: 11000000 INFO @ Sun, 21 Jun 2020 18:18:34: 6000000 INFO @ Sun, 21 Jun 2020 18:18:36: 1000000 INFO @ Sun, 21 Jun 2020 18:18:36: 12000000 INFO @ Sun, 21 Jun 2020 18:18:39: 7000000 INFO @ Sun, 21 Jun 2020 18:18:41: 2000000 INFO @ Sun, 21 Jun 2020 18:18:41: 13000000 INFO @ Sun, 21 Jun 2020 18:18:45: 8000000 INFO @ Sun, 21 Jun 2020 18:18:46: 3000000 INFO @ Sun, 21 Jun 2020 18:18:47: 14000000 INFO @ Sun, 21 Jun 2020 18:18:51: 9000000 INFO @ Sun, 21 Jun 2020 18:18:52: 4000000 INFO @ Sun, 21 Jun 2020 18:18:52: 15000000 INFO @ Sun, 21 Jun 2020 18:18:57: 10000000 INFO @ Sun, 21 Jun 2020 18:18:57: 5000000 INFO @ Sun, 21 Jun 2020 18:18:57: 16000000 INFO @ Sun, 21 Jun 2020 18:19:02: 11000000 INFO @ Sun, 21 Jun 2020 18:19:02: 6000000 INFO @ Sun, 21 Jun 2020 18:19:02: 17000000 INFO @ Sun, 21 Jun 2020 18:19:07: 12000000 INFO @ Sun, 21 Jun 2020 18:19:07: 7000000 INFO @ Sun, 21 Jun 2020 18:19:08: 18000000 INFO @ Sun, 21 Jun 2020 18:19:13: 13000000 INFO @ Sun, 21 Jun 2020 18:19:13: 8000000 INFO @ Sun, 21 Jun 2020 18:19:13: 19000000 INFO @ Sun, 21 Jun 2020 18:19:18: 14000000 INFO @ Sun, 21 Jun 2020 18:19:18: 9000000 INFO @ Sun, 21 Jun 2020 18:19:19: 20000000 INFO @ Sun, 21 Jun 2020 18:19:23: 15000000 INFO @ Sun, 21 Jun 2020 18:19:24: 10000000 INFO @ Sun, 21 Jun 2020 18:19:24: 21000000 INFO @ Sun, 21 Jun 2020 18:19:29: 11000000 INFO @ Sun, 21 Jun 2020 18:19:29: 16000000 INFO @ Sun, 21 Jun 2020 18:19:29: 22000000 INFO @ Sun, 21 Jun 2020 18:19:34: 12000000 INFO @ Sun, 21 Jun 2020 18:19:34: 17000000 INFO @ Sun, 21 Jun 2020 18:19:35: 23000000 INFO @ Sun, 21 Jun 2020 18:19:40: 18000000 INFO @ Sun, 21 Jun 2020 18:19:40: 13000000 INFO @ Sun, 21 Jun 2020 18:19:40: 24000000 INFO @ Sun, 21 Jun 2020 18:19:45: 19000000 INFO @ Sun, 21 Jun 2020 18:19:45: 14000000 INFO @ Sun, 21 Jun 2020 18:19:46: 25000000 INFO @ Sun, 21 Jun 2020 18:19:51: 20000000 INFO @ Sun, 21 Jun 2020 18:19:51: 15000000 INFO @ Sun, 21 Jun 2020 18:19:52: 26000000 INFO @ Sun, 21 Jun 2020 18:19:56: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:19:56: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:19:56: #1 total tags in treatment: 26677450 INFO @ Sun, 21 Jun 2020 18:19:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:19:56: #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 18:19:56: 16000000 INFO @ Sun, 21 Jun 2020 18:19:56: #1 tags after filtering in treatment: 26677413 INFO @ Sun, 21 Jun 2020 18:19:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:19:56: #1 finished! INFO @ Sun, 21 Jun 2020 18:19:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:19:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:19:56: 21000000 INFO @ Sun, 21 Jun 2020 18:19:59: #2 number of paired peaks: 3420 INFO @ Sun, 21 Jun 2020 18:19:59: start model_add_line... INFO @ Sun, 21 Jun 2020 18:19:59: start X-correlation... INFO @ Sun, 21 Jun 2020 18:19:59: end of X-cor INFO @ Sun, 21 Jun 2020 18:19:59: #2 finished! INFO @ Sun, 21 Jun 2020 18:19:59: #2 predicted fragment length is 69 bps INFO @ Sun, 21 Jun 2020 18:19:59: #2 alternative fragment length(s) may be 2,69 bps INFO @ Sun, 21 Jun 2020 18:19:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1361346/SRX1361346.05_model.r WARNING @ Sun, 21 Jun 2020 18:19:59: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:19:59: #2 You may need to consider one of the other alternative d(s): 2,69 WARNING @ Sun, 21 Jun 2020 18:19:59: #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 18:19:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:19:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:20:02: 17000000 INFO @ Sun, 21 Jun 2020 18:20:02: 22000000 INFO @ Sun, 21 Jun 2020 18:20:07: 18000000 INFO @ Sun, 21 Jun 2020 18:20:08: 23000000 INFO @ Sun, 21 Jun 2020 18:20:13: 19000000 INFO @ Sun, 21 Jun 2020 18:20:15: 24000000 INFO @ Sun, 21 Jun 2020 18:20:19: 20000000 INFO @ Sun, 21 Jun 2020 18:20:21: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:20:25: 21000000 INFO @ Sun, 21 Jun 2020 18:20:27: 26000000 INFO @ Sun, 21 Jun 2020 18:20:31: 22000000 INFO @ Sun, 21 Jun 2020 18:20:31: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:20:31: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:20:31: #1 total tags in treatment: 26677450 INFO @ Sun, 21 Jun 2020 18:20:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:20:31: #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 18:20:32: #1 tags after filtering in treatment: 26677413 INFO @ Sun, 21 Jun 2020 18:20:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:20:32: #1 finished! INFO @ Sun, 21 Jun 2020 18:20:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:20:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:20:34: #2 number of paired peaks: 3420 INFO @ Sun, 21 Jun 2020 18:20:34: start model_add_line... INFO @ Sun, 21 Jun 2020 18:20:34: start X-correlation... INFO @ Sun, 21 Jun 2020 18:20:34: end of X-cor INFO @ Sun, 21 Jun 2020 18:20:34: #2 finished! INFO @ Sun, 21 Jun 2020 18:20:34: #2 predicted fragment length is 69 bps INFO @ Sun, 21 Jun 2020 18:20:34: #2 alternative fragment length(s) may be 2,69 bps INFO @ Sun, 21 Jun 2020 18:20:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1361346/SRX1361346.10_model.r WARNING @ Sun, 21 Jun 2020 18:20:34: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:20:34: #2 You may need to consider one of the other alternative d(s): 2,69 WARNING @ Sun, 21 Jun 2020 18:20:34: #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 18:20:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:20:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:20:36: 23000000 INFO @ Sun, 21 Jun 2020 18:20:42: 24000000 INFO @ Sun, 21 Jun 2020 18:20:47: 25000000 INFO @ Sun, 21 Jun 2020 18:20:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:20:52: 26000000 INFO @ Sun, 21 Jun 2020 18:20:56: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:20:56: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:20:56: #1 total tags in treatment: 26677450 INFO @ Sun, 21 Jun 2020 18:20:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:20:56: #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 18:20:57: #1 tags after filtering in treatment: 26677413 INFO @ Sun, 21 Jun 2020 18:20:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:20:57: #1 finished! INFO @ Sun, 21 Jun 2020 18:20:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:20:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:20:59: #2 number of paired peaks: 3420 INFO @ Sun, 21 Jun 2020 18:20:59: start model_add_line... INFO @ Sun, 21 Jun 2020 18:20:59: start X-correlation... INFO @ Sun, 21 Jun 2020 18:20:59: end of X-cor INFO @ Sun, 21 Jun 2020 18:20:59: #2 finished! INFO @ Sun, 21 Jun 2020 18:20:59: #2 predicted fragment length is 69 bps INFO @ Sun, 21 Jun 2020 18:20:59: #2 alternative fragment length(s) may be 2,69 bps INFO @ Sun, 21 Jun 2020 18:20:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1361346/SRX1361346.20_model.r WARNING @ Sun, 21 Jun 2020 18:20:59: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:20:59: #2 You may need to consider one of the other alternative d(s): 2,69 WARNING @ Sun, 21 Jun 2020 18:20:59: #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 18:20:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:20:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:21:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1361346/SRX1361346.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:21:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1361346/SRX1361346.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:21:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1361346/SRX1361346.05_summits.bed INFO @ Sun, 21 Jun 2020 18:21:13: Done! pass1 - making usageList (1182 chroms): 2 millis pass2 - checking and writing primary data (11067 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:21:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:21:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1361346/SRX1361346.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:21:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1361346/SRX1361346.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:21:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1361346/SRX1361346.10_summits.bed INFO @ Sun, 21 Jun 2020 18:21:48: Done! pass1 - making usageList (1072 chroms): 2 millis pass2 - checking and writing primary data (5682 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:21:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:22:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1361346/SRX1361346.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:22:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1361346/SRX1361346.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:22:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1361346/SRX1361346.20_summits.bed INFO @ Sun, 21 Jun 2020 18:22:13: Done! pass1 - making usageList (875 chroms): 1 millis pass2 - checking and writing primary data (3000 records, 4 fields): 26 millis CompletedMACS2peakCalling