Job ID = 6458915 SRX = SRX5775920 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:46:55 prefetch.2.10.7: 1) Downloading 'SRR8997123'... 2020-06-21T12:46:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:49:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:49:56 prefetch.2.10.7: 1) 'SRR8997123' was downloaded successfully Read 20242183 spots for SRR8997123/SRR8997123.sra Written 20242183 spots for SRR8997123/SRR8997123.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: 00:07:36 20242183 reads; of these: 20242183 (100.00%) were unpaired; of these: 824874 (4.08%) aligned 0 times 13922199 (68.78%) aligned exactly 1 time 5495110 (27.15%) aligned >1 times 95.92% overall alignment rate Time searching: 00:07:36 Overall time: 00:07:36 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 8 files... [bam_rmdupse_core] 7882267 / 19417309 = 0.4059 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 22:03:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775920/SRX5775920.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775920/SRX5775920.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775920/SRX5775920.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775920/SRX5775920.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 22:03:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:03:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:03:10: 1000000 INFO @ Sun, 21 Jun 2020 22:03:17: 2000000 INFO @ Sun, 21 Jun 2020 22:03:23: 3000000 INFO @ Sun, 21 Jun 2020 22:03:30: 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 22:03:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775920/SRX5775920.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775920/SRX5775920.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775920/SRX5775920.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775920/SRX5775920.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 22:03:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:03:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:03:37: 5000000 INFO @ Sun, 21 Jun 2020 22:03:40: 1000000 INFO @ Sun, 21 Jun 2020 22:03:43: 6000000 INFO @ Sun, 21 Jun 2020 22:03:47: 2000000 INFO @ Sun, 21 Jun 2020 22:03:50: 7000000 INFO @ Sun, 21 Jun 2020 22:03:54: 3000000 INFO @ Sun, 21 Jun 2020 22:03:57: 8000000 INFO @ Sun, 21 Jun 2020 22:04:01: 4000000 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 22:04:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775920/SRX5775920.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775920/SRX5775920.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775920/SRX5775920.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775920/SRX5775920.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 22:04:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:04:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:04:04: 9000000 INFO @ Sun, 21 Jun 2020 22:04:08: 5000000 INFO @ Sun, 21 Jun 2020 22:04:10: 1000000 INFO @ Sun, 21 Jun 2020 22:04:11: 10000000 INFO @ Sun, 21 Jun 2020 22:04:15: 6000000 INFO @ Sun, 21 Jun 2020 22:04:18: 2000000 INFO @ Sun, 21 Jun 2020 22:04:18: 11000000 INFO @ Sun, 21 Jun 2020 22:04:22: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:04:22: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:04:22: #1 total tags in treatment: 11535042 INFO @ Sun, 21 Jun 2020 22:04:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:04:22: #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 22:04:22: 7000000 INFO @ Sun, 21 Jun 2020 22:04:22: #1 tags after filtering in treatment: 11535038 INFO @ Sun, 21 Jun 2020 22:04:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:04:22: #1 finished! INFO @ Sun, 21 Jun 2020 22:04:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:04:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:04:23: #2 number of paired peaks: 1006 INFO @ Sun, 21 Jun 2020 22:04:23: start model_add_line... INFO @ Sun, 21 Jun 2020 22:04:23: start X-correlation... INFO @ Sun, 21 Jun 2020 22:04:23: end of X-cor INFO @ Sun, 21 Jun 2020 22:04:23: #2 finished! INFO @ Sun, 21 Jun 2020 22:04:23: #2 predicted fragment length is 69 bps INFO @ Sun, 21 Jun 2020 22:04:23: #2 alternative fragment length(s) may be 4,69 bps INFO @ Sun, 21 Jun 2020 22:04:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775920/SRX5775920.05_model.r WARNING @ Sun, 21 Jun 2020 22:04:23: #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 22:04:23: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Sun, 21 Jun 2020 22:04:23: #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 22:04:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:04:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:04:25: 3000000 INFO @ Sun, 21 Jun 2020 22:04:28: 8000000 INFO @ Sun, 21 Jun 2020 22:04:32: 4000000 INFO @ Sun, 21 Jun 2020 22:04:35: 9000000 INFO @ Sun, 21 Jun 2020 22:04:39: 5000000 INFO @ Sun, 21 Jun 2020 22:04:42: 10000000 INFO @ Sun, 21 Jun 2020 22:04:46: 6000000 INFO @ Sun, 21 Jun 2020 22:04:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:04:49: 11000000 INFO @ Sun, 21 Jun 2020 22:04:52: 7000000 INFO @ Sun, 21 Jun 2020 22:04:53: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:04:53: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:04:53: #1 total tags in treatment: 11535042 INFO @ Sun, 21 Jun 2020 22:04:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:04:53: #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 22:04:53: #1 tags after filtering in treatment: 11535038 INFO @ Sun, 21 Jun 2020 22:04:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:04:53: #1 finished! INFO @ Sun, 21 Jun 2020 22:04:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:04:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:04:54: #2 number of paired peaks: 1006 INFO @ Sun, 21 Jun 2020 22:04:54: start model_add_line... INFO @ Sun, 21 Jun 2020 22:04:54: start X-correlation... INFO @ Sun, 21 Jun 2020 22:04:54: end of X-cor INFO @ Sun, 21 Jun 2020 22:04:54: #2 finished! INFO @ Sun, 21 Jun 2020 22:04:54: #2 predicted fragment length is 69 bps INFO @ Sun, 21 Jun 2020 22:04:54: #2 alternative fragment length(s) may be 4,69 bps INFO @ Sun, 21 Jun 2020 22:04:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775920/SRX5775920.10_model.r WARNING @ Sun, 21 Jun 2020 22:04:54: #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 22:04:54: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Sun, 21 Jun 2020 22:04:54: #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 22:04:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:04:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:04:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775920/SRX5775920.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:04:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775920/SRX5775920.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:04:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775920/SRX5775920.05_summits.bed INFO @ Sun, 21 Jun 2020 22:04:57: Done! pass1 - making usageList (727 chroms): 2 millis pass2 - checking and writing primary data (2345 records, 4 fields): 20 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:04:59: 8000000 INFO @ Sun, 21 Jun 2020 22:05:06: 9000000 INFO @ Sun, 21 Jun 2020 22:05:13: 10000000 INFO @ Sun, 21 Jun 2020 22:05:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:05:20: 11000000 INFO @ Sun, 21 Jun 2020 22:05:23: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:05:23: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:05:23: #1 total tags in treatment: 11535042 INFO @ Sun, 21 Jun 2020 22:05:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:05:23: #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 22:05:24: #1 tags after filtering in treatment: 11535038 INFO @ Sun, 21 Jun 2020 22:05:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:05:24: #1 finished! INFO @ Sun, 21 Jun 2020 22:05:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:05:24: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:05:24: #2 number of paired peaks: 1006 INFO @ Sun, 21 Jun 2020 22:05:24: start model_add_line... INFO @ Sun, 21 Jun 2020 22:05:25: start X-correlation... INFO @ Sun, 21 Jun 2020 22:05:25: end of X-cor INFO @ Sun, 21 Jun 2020 22:05:25: #2 finished! INFO @ Sun, 21 Jun 2020 22:05:25: #2 predicted fragment length is 69 bps INFO @ Sun, 21 Jun 2020 22:05:25: #2 alternative fragment length(s) may be 4,69 bps INFO @ Sun, 21 Jun 2020 22:05:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775920/SRX5775920.20_model.r WARNING @ Sun, 21 Jun 2020 22:05:25: #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 22:05:25: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Sun, 21 Jun 2020 22:05:25: #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 22:05:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:05:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:05:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775920/SRX5775920.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:05:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775920/SRX5775920.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:05:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775920/SRX5775920.10_summits.bed INFO @ Sun, 21 Jun 2020 22:05:28: Done! pass1 - making usageList (621 chroms): 1 millis pass2 - checking and writing primary data (1809 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:05:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:05:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775920/SRX5775920.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:05:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775920/SRX5775920.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:05:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775920/SRX5775920.20_summits.bed INFO @ Sun, 21 Jun 2020 22:05:59: Done! pass1 - making usageList (474 chroms): 1 millis pass2 - checking and writing primary data (1283 records, 4 fields): 15 millis CompletedMACS2peakCalling