Job ID = 6454348 SRX = SRX201884 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:12:12 prefetch.2.10.7: 1) Downloading 'SRR609674'... 2020-06-21T09:12:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:26:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:26:24 prefetch.2.10.7: 1) 'SRR609674' was downloaded successfully Read 32593052 spots for SRR609674/SRR609674.sra Written 32593052 spots for SRR609674/SRR609674.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: 00:26:47 32593052 reads; of these: 32593052 (100.00%) were unpaired; of these: 1379454 (4.23%) aligned 0 times 10251746 (31.45%) aligned exactly 1 time 20961852 (64.31%) aligned >1 times 95.77% overall alignment rate Time searching: 00:26:47 Overall time: 00:26:47 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 16 files... [bam_rmdupse_core] 12008299 / 31213598 = 0.3847 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 19:06:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX201884/SRX201884.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX201884/SRX201884.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX201884/SRX201884.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX201884/SRX201884.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 19:06:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:06:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:06:51: 1000000 INFO @ Sun, 21 Jun 2020 19:06:58: 2000000 INFO @ Sun, 21 Jun 2020 19:07:06: 3000000 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 19:07:13: 4000000 INFO @ Sun, 21 Jun 2020 19:07:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX201884/SRX201884.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX201884/SRX201884.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX201884/SRX201884.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX201884/SRX201884.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 19:07:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:07:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:07:21: 5000000 INFO @ Sun, 21 Jun 2020 19:07:23: 1000000 INFO @ Sun, 21 Jun 2020 19:07:29: 6000000 INFO @ Sun, 21 Jun 2020 19:07:32: 2000000 INFO @ Sun, 21 Jun 2020 19:07:38: 7000000 INFO @ Sun, 21 Jun 2020 19:07:41: 3000000 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 19:07:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX201884/SRX201884.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX201884/SRX201884.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX201884/SRX201884.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX201884/SRX201884.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 19:07:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:07:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:07:47: 8000000 INFO @ Sun, 21 Jun 2020 19:07:50: 4000000 INFO @ Sun, 21 Jun 2020 19:07:53: 1000000 INFO @ Sun, 21 Jun 2020 19:07:56: 9000000 INFO @ Sun, 21 Jun 2020 19:08:00: 5000000 INFO @ Sun, 21 Jun 2020 19:08:02: 2000000 INFO @ Sun, 21 Jun 2020 19:08:05: 10000000 INFO @ Sun, 21 Jun 2020 19:08:09: 6000000 INFO @ Sun, 21 Jun 2020 19:08:11: 3000000 INFO @ Sun, 21 Jun 2020 19:08:14: 11000000 INFO @ Sun, 21 Jun 2020 19:08:18: 7000000 INFO @ Sun, 21 Jun 2020 19:08:19: 4000000 INFO @ Sun, 21 Jun 2020 19:08:23: 12000000 INFO @ Sun, 21 Jun 2020 19:08:28: 5000000 INFO @ Sun, 21 Jun 2020 19:08:28: 8000000 INFO @ Sun, 21 Jun 2020 19:08:32: 13000000 INFO @ Sun, 21 Jun 2020 19:08:36: 6000000 INFO @ Sun, 21 Jun 2020 19:08:37: 9000000 INFO @ Sun, 21 Jun 2020 19:08:41: 14000000 INFO @ Sun, 21 Jun 2020 19:08:45: 7000000 INFO @ Sun, 21 Jun 2020 19:08:47: 10000000 INFO @ Sun, 21 Jun 2020 19:08:50: 15000000 INFO @ Sun, 21 Jun 2020 19:08:53: 8000000 INFO @ Sun, 21 Jun 2020 19:08:56: 11000000 INFO @ Sun, 21 Jun 2020 19:08:59: 16000000 INFO @ Sun, 21 Jun 2020 19:09:02: 9000000 INFO @ Sun, 21 Jun 2020 19:09:06: 12000000 INFO @ Sun, 21 Jun 2020 19:09:09: 17000000 INFO @ Sun, 21 Jun 2020 19:09:11: 10000000 INFO @ Sun, 21 Jun 2020 19:09:15: 13000000 INFO @ Sun, 21 Jun 2020 19:09:18: 18000000 INFO @ Sun, 21 Jun 2020 19:09:19: 11000000 INFO @ Sun, 21 Jun 2020 19:09:24: 14000000 INFO @ Sun, 21 Jun 2020 19:09:28: 19000000 INFO @ Sun, 21 Jun 2020 19:09:28: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:09:30: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 19:09:30: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 19:09:30: #1 total tags in treatment: 19205299 INFO @ Sun, 21 Jun 2020 19:09:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:09:30: #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 19:09:31: #1 tags after filtering in treatment: 19205222 INFO @ Sun, 21 Jun 2020 19:09:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:09:31: #1 finished! INFO @ Sun, 21 Jun 2020 19:09:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:09:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:09:33: #2 number of paired peaks: 6351 INFO @ Sun, 21 Jun 2020 19:09:33: start model_add_line... INFO @ Sun, 21 Jun 2020 19:09:33: start X-correlation... INFO @ Sun, 21 Jun 2020 19:09:33: end of X-cor INFO @ Sun, 21 Jun 2020 19:09:33: #2 finished! INFO @ Sun, 21 Jun 2020 19:09:33: #2 predicted fragment length is 113 bps INFO @ Sun, 21 Jun 2020 19:09:33: #2 alternative fragment length(s) may be 3,113 bps INFO @ Sun, 21 Jun 2020 19:09:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX201884/SRX201884.05_model.r WARNING @ Sun, 21 Jun 2020 19:09:33: #2 Since the d (113) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:09:33: #2 You may need to consider one of the other alternative d(s): 3,113 WARNING @ Sun, 21 Jun 2020 19:09:33: #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 19:09:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:09:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:09:34: 15000000 INFO @ Sun, 21 Jun 2020 19:09:37: 13000000 INFO @ Sun, 21 Jun 2020 19:09:44: 16000000 INFO @ Sun, 21 Jun 2020 19:09:46: 14000000 INFO @ Sun, 21 Jun 2020 19:09:53: 17000000 INFO @ Sun, 21 Jun 2020 19:09:55: 15000000 INFO @ Sun, 21 Jun 2020 19:10:03: 18000000 INFO @ Sun, 21 Jun 2020 19:10:03: 16000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:10:12: 17000000 INFO @ Sun, 21 Jun 2020 19:10:13: 19000000 INFO @ Sun, 21 Jun 2020 19:10:15: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 19:10:15: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 19:10:15: #1 total tags in treatment: 19205299 INFO @ Sun, 21 Jun 2020 19:10:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:10:15: #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 19:10:15: #1 tags after filtering in treatment: 19205222 INFO @ Sun, 21 Jun 2020 19:10:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:10:15: #1 finished! INFO @ Sun, 21 Jun 2020 19:10:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:10:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:10:17: #2 number of paired peaks: 6351 INFO @ Sun, 21 Jun 2020 19:10:17: start model_add_line... INFO @ Sun, 21 Jun 2020 19:10:18: start X-correlation... INFO @ Sun, 21 Jun 2020 19:10:18: end of X-cor INFO @ Sun, 21 Jun 2020 19:10:18: #2 finished! INFO @ Sun, 21 Jun 2020 19:10:18: #2 predicted fragment length is 113 bps INFO @ Sun, 21 Jun 2020 19:10:18: #2 alternative fragment length(s) may be 3,113 bps INFO @ Sun, 21 Jun 2020 19:10:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX201884/SRX201884.10_model.r WARNING @ Sun, 21 Jun 2020 19:10:18: #2 Since the d (113) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:10:18: #2 You may need to consider one of the other alternative d(s): 3,113 WARNING @ Sun, 21 Jun 2020 19:10:18: #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 19:10:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:10:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:10:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:10:19: 18000000 INFO @ Sun, 21 Jun 2020 19:10:27: 19000000 INFO @ Sun, 21 Jun 2020 19:10:29: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 19:10:29: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 19:10:29: #1 total tags in treatment: 19205299 INFO @ Sun, 21 Jun 2020 19:10:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:10:29: #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 19:10:29: #1 tags after filtering in treatment: 19205222 INFO @ Sun, 21 Jun 2020 19:10:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:10:29: #1 finished! INFO @ Sun, 21 Jun 2020 19:10:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:10:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:10:31: #2 number of paired peaks: 6351 INFO @ Sun, 21 Jun 2020 19:10:31: start model_add_line... INFO @ Sun, 21 Jun 2020 19:10:32: start X-correlation... INFO @ Sun, 21 Jun 2020 19:10:32: end of X-cor INFO @ Sun, 21 Jun 2020 19:10:32: #2 finished! INFO @ Sun, 21 Jun 2020 19:10:32: #2 predicted fragment length is 113 bps INFO @ Sun, 21 Jun 2020 19:10:32: #2 alternative fragment length(s) may be 3,113 bps INFO @ Sun, 21 Jun 2020 19:10:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX201884/SRX201884.20_model.r WARNING @ Sun, 21 Jun 2020 19:10:32: #2 Since the d (113) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:10:32: #2 You may need to consider one of the other alternative d(s): 3,113 WARNING @ Sun, 21 Jun 2020 19:10:32: #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 19:10:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:10:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:10:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX201884/SRX201884.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:10:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX201884/SRX201884.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:10:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX201884/SRX201884.05_summits.bed INFO @ Sun, 21 Jun 2020 19:10:39: Done! pass1 - making usageList (1090 chroms): 3 millis pass2 - checking and writing primary data (11036 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:11:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:11:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:11:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX201884/SRX201884.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:11:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX201884/SRX201884.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:11:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX201884/SRX201884.10_summits.bed INFO @ Sun, 21 Jun 2020 19:11:23: Done! pass1 - making usageList (1006 chroms): 2 millis pass2 - checking and writing primary data (6351 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:11:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX201884/SRX201884.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:11:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX201884/SRX201884.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:11:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX201884/SRX201884.20_summits.bed INFO @ Sun, 21 Jun 2020 19:11:36: Done! pass1 - making usageList (864 chroms): 2 millis pass2 - checking and writing primary data (3016 records, 4 fields): 26 millis CompletedMACS2peakCalling