Job ID = 6451963 SRX = ERX102368 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:12:47 prefetch.2.10.7: 1) Downloading 'ERR126224'... 2020-06-21T07:12:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:24:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:24:11 prefetch.2.10.7: 1) 'ERR126224' was downloaded successfully Read 24802445 spots for ERR126224/ERR126224.sra Written 24802445 spots for ERR126224/ERR126224.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: 00:07:05 24802445 reads; of these: 24802445 (100.00%) were unpaired; of these: 2596953 (10.47%) aligned 0 times 20995871 (84.65%) aligned exactly 1 time 1209621 (4.88%) aligned >1 times 89.53% overall alignment rate Time searching: 00:07:05 Overall time: 00:07:05 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 12 files... [bam_rmdupse_core] 10419036 / 22205492 = 0.4692 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 16:38:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX102368/ERX102368.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX102368/ERX102368.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX102368/ERX102368.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX102368/ERX102368.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 16:38:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:38:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:38:32: 1000000 INFO @ Sun, 21 Jun 2020 16:38:38: 2000000 INFO @ Sun, 21 Jun 2020 16:38:44: 3000000 INFO @ Sun, 21 Jun 2020 16:38:50: 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 16:38:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX102368/ERX102368.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX102368/ERX102368.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX102368/ERX102368.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX102368/ERX102368.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 16:38:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:38:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:38:56: 5000000 INFO @ Sun, 21 Jun 2020 16:39:02: 6000000 INFO @ Sun, 21 Jun 2020 16:39:02: 1000000 INFO @ Sun, 21 Jun 2020 16:39:08: 2000000 INFO @ Sun, 21 Jun 2020 16:39:09: 7000000 INFO @ Sun, 21 Jun 2020 16:39:15: 3000000 INFO @ Sun, 21 Jun 2020 16:39:15: 8000000 INFO @ Sun, 21 Jun 2020 16:39:21: 4000000 INFO @ Sun, 21 Jun 2020 16:39:21: 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 16:39:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX102368/ERX102368.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX102368/ERX102368.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX102368/ERX102368.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX102368/ERX102368.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 16:39:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:39:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:39:27: 5000000 INFO @ Sun, 21 Jun 2020 16:39:28: 10000000 INFO @ Sun, 21 Jun 2020 16:39:34: 1000000 INFO @ Sun, 21 Jun 2020 16:39:35: 6000000 INFO @ Sun, 21 Jun 2020 16:39:36: 11000000 INFO @ Sun, 21 Jun 2020 16:39:42: 2000000 INFO @ Sun, 21 Jun 2020 16:39:42: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 16:39:42: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 16:39:42: #1 total tags in treatment: 11786456 INFO @ Sun, 21 Jun 2020 16:39:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:39:42: #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 16:39:42: #1 tags after filtering in treatment: 11785857 INFO @ Sun, 21 Jun 2020 16:39:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:39:42: #1 finished! INFO @ Sun, 21 Jun 2020 16:39:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:39:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:39:43: 7000000 INFO @ Sun, 21 Jun 2020 16:39:44: #2 number of paired peaks: 6642 INFO @ Sun, 21 Jun 2020 16:39:44: start model_add_line... INFO @ Sun, 21 Jun 2020 16:39:44: start X-correlation... INFO @ Sun, 21 Jun 2020 16:39:44: end of X-cor INFO @ Sun, 21 Jun 2020 16:39:44: #2 finished! INFO @ Sun, 21 Jun 2020 16:39:44: #2 predicted fragment length is 147 bps INFO @ Sun, 21 Jun 2020 16:39:44: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 21 Jun 2020 16:39:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX102368/ERX102368.05_model.r WARNING @ Sun, 21 Jun 2020 16:39:44: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:39:44: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Sun, 21 Jun 2020 16:39:44: #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 16:39:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:39:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:39:50: 3000000 INFO @ Sun, 21 Jun 2020 16:39:50: 8000000 INFO @ Sun, 21 Jun 2020 16:39:57: 9000000 INFO @ Sun, 21 Jun 2020 16:39:58: 4000000 INFO @ Sun, 21 Jun 2020 16:40:05: 10000000 INFO @ Sun, 21 Jun 2020 16:40:06: 5000000 INFO @ Sun, 21 Jun 2020 16:40:13: 11000000 INFO @ Sun, 21 Jun 2020 16:40:14: 6000000 INFO @ Sun, 21 Jun 2020 16:40:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:40:19: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 16:40:19: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 16:40:19: #1 total tags in treatment: 11786456 INFO @ Sun, 21 Jun 2020 16:40:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:40:19: #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 16:40:19: #1 tags after filtering in treatment: 11785857 INFO @ Sun, 21 Jun 2020 16:40:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:40:19: #1 finished! INFO @ Sun, 21 Jun 2020 16:40:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:40:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:40:20: #2 number of paired peaks: 6642 INFO @ Sun, 21 Jun 2020 16:40:20: start model_add_line... INFO @ Sun, 21 Jun 2020 16:40:20: start X-correlation... INFO @ Sun, 21 Jun 2020 16:40:20: end of X-cor INFO @ Sun, 21 Jun 2020 16:40:20: #2 finished! INFO @ Sun, 21 Jun 2020 16:40:20: #2 predicted fragment length is 147 bps INFO @ Sun, 21 Jun 2020 16:40:20: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 21 Jun 2020 16:40:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX102368/ERX102368.10_model.r WARNING @ Sun, 21 Jun 2020 16:40:20: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:40:20: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Sun, 21 Jun 2020 16:40:20: #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 16:40:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:40:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:40:22: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:40:29: 8000000 INFO @ Sun, 21 Jun 2020 16:40:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX102368/ERX102368.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:40:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX102368/ERX102368.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:40:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX102368/ERX102368.05_summits.bed INFO @ Sun, 21 Jun 2020 16:40:33: Done! pass1 - making usageList (59 chroms): 3 millis pass2 - checking and writing primary data (10712 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:40:37: 9000000 INFO @ Sun, 21 Jun 2020 16:40:45: 10000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:40:52: 11000000 INFO @ Sun, 21 Jun 2020 16:40:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:40:58: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 16:40:58: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 16:40:58: #1 total tags in treatment: 11786456 INFO @ Sun, 21 Jun 2020 16:40:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:40:58: #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 16:40:59: #1 tags after filtering in treatment: 11785857 INFO @ Sun, 21 Jun 2020 16:40:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:40:59: #1 finished! INFO @ Sun, 21 Jun 2020 16:40:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:40:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:41:00: #2 number of paired peaks: 6642 INFO @ Sun, 21 Jun 2020 16:41:00: start model_add_line... INFO @ Sun, 21 Jun 2020 16:41:00: start X-correlation... INFO @ Sun, 21 Jun 2020 16:41:00: end of X-cor INFO @ Sun, 21 Jun 2020 16:41:00: #2 finished! INFO @ Sun, 21 Jun 2020 16:41:00: #2 predicted fragment length is 147 bps INFO @ Sun, 21 Jun 2020 16:41:00: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 21 Jun 2020 16:41:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX102368/ERX102368.20_model.r WARNING @ Sun, 21 Jun 2020 16:41:00: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:41:00: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Sun, 21 Jun 2020 16:41:00: #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 16:41:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:41:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:41:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX102368/ERX102368.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:41:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX102368/ERX102368.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:41:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX102368/ERX102368.10_summits.bed INFO @ Sun, 21 Jun 2020 16:41:10: Done! pass1 - making usageList (42 chroms): 2 millis pass2 - checking and writing primary data (8438 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:41:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:41:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX102368/ERX102368.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:41:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX102368/ERX102368.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:41:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX102368/ERX102368.20_summits.bed INFO @ Sun, 21 Jun 2020 16:41:48: Done! pass1 - making usageList (26 chroms): 1 millis pass2 - checking and writing primary data (6375 records, 4 fields): 8 millis CompletedMACS2peakCalling