Job ID = 6452995 SRX = SRX089334 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:09:34 prefetch.2.10.7: 1) Downloading 'SRR327605'... 2020-06-21T08:09:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:17:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:17:52 prefetch.2.10.7: 1) 'SRR327605' was downloaded successfully Read 42776703 spots for SRR327605/SRR327605.sra Written 42776703 spots for SRR327605/SRR327605.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: 00:07:23 42776703 reads; of these: 42776703 (100.00%) were unpaired; of these: 11881364 (27.78%) aligned 0 times 24189764 (56.55%) aligned exactly 1 time 6705575 (15.68%) aligned >1 times 72.22% overall alignment rate Time searching: 00:07:23 Overall time: 00:07:23 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] 10745918 / 30895339 = 0.3478 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 17:33:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX089334/SRX089334.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX089334/SRX089334.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX089334/SRX089334.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX089334/SRX089334.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 17:33:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:33:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:33:04: 1000000 INFO @ Sun, 21 Jun 2020 17:33:09: 2000000 INFO @ Sun, 21 Jun 2020 17:33:13: 3000000 INFO @ Sun, 21 Jun 2020 17:33:18: 4000000 INFO @ Sun, 21 Jun 2020 17:33:22: 5000000 INFO @ Sun, 21 Jun 2020 17:33:27: 6000000 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 17:33:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX089334/SRX089334.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX089334/SRX089334.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX089334/SRX089334.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX089334/SRX089334.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 17:33:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:33:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:33:32: 7000000 INFO @ Sun, 21 Jun 2020 17:33:34: 1000000 INFO @ Sun, 21 Jun 2020 17:33:36: 8000000 INFO @ Sun, 21 Jun 2020 17:33:39: 2000000 INFO @ Sun, 21 Jun 2020 17:33:41: 9000000 INFO @ Sun, 21 Jun 2020 17:33:43: 3000000 INFO @ Sun, 21 Jun 2020 17:33:45: 10000000 INFO @ Sun, 21 Jun 2020 17:33:48: 4000000 INFO @ Sun, 21 Jun 2020 17:33:50: 11000000 INFO @ Sun, 21 Jun 2020 17:33:53: 5000000 INFO @ Sun, 21 Jun 2020 17:33:54: 12000000 INFO @ Sun, 21 Jun 2020 17:33:57: 6000000 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 17:33:59: 13000000 INFO @ Sun, 21 Jun 2020 17:34:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX089334/SRX089334.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX089334/SRX089334.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX089334/SRX089334.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX089334/SRX089334.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 17:34:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:34:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:34:02: 7000000 INFO @ Sun, 21 Jun 2020 17:34:03: 14000000 INFO @ Sun, 21 Jun 2020 17:34:04: 1000000 INFO @ Sun, 21 Jun 2020 17:34:07: 8000000 INFO @ Sun, 21 Jun 2020 17:34:08: 15000000 INFO @ Sun, 21 Jun 2020 17:34:09: 2000000 INFO @ Sun, 21 Jun 2020 17:34:11: 9000000 INFO @ Sun, 21 Jun 2020 17:34:13: 16000000 INFO @ Sun, 21 Jun 2020 17:34:13: 3000000 INFO @ Sun, 21 Jun 2020 17:34:16: 10000000 INFO @ Sun, 21 Jun 2020 17:34:18: 17000000 INFO @ Sun, 21 Jun 2020 17:34:18: 4000000 INFO @ Sun, 21 Jun 2020 17:34:20: 11000000 INFO @ Sun, 21 Jun 2020 17:34:22: 18000000 INFO @ Sun, 21 Jun 2020 17:34:22: 5000000 INFO @ Sun, 21 Jun 2020 17:34:25: 12000000 INFO @ Sun, 21 Jun 2020 17:34:27: 19000000 INFO @ Sun, 21 Jun 2020 17:34:27: 6000000 INFO @ Sun, 21 Jun 2020 17:34:30: 13000000 INFO @ Sun, 21 Jun 2020 17:34:32: 7000000 INFO @ Sun, 21 Jun 2020 17:34:32: 20000000 INFO @ Sun, 21 Jun 2020 17:34:33: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:34:33: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:34:33: #1 total tags in treatment: 20149421 INFO @ Sun, 21 Jun 2020 17:34:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:34:33: #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 17:34:33: #1 tags after filtering in treatment: 20149348 INFO @ Sun, 21 Jun 2020 17:34:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:34:33: #1 finished! INFO @ Sun, 21 Jun 2020 17:34:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:34:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:34:34: 14000000 INFO @ Sun, 21 Jun 2020 17:34:35: #2 number of paired peaks: 2360 INFO @ Sun, 21 Jun 2020 17:34:35: start model_add_line... INFO @ Sun, 21 Jun 2020 17:34:35: start X-correlation... INFO @ Sun, 21 Jun 2020 17:34:35: end of X-cor INFO @ Sun, 21 Jun 2020 17:34:35: #2 finished! INFO @ Sun, 21 Jun 2020 17:34:35: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 17:34:35: #2 alternative fragment length(s) may be 4,58 bps INFO @ Sun, 21 Jun 2020 17:34:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX089334/SRX089334.05_model.r WARNING @ Sun, 21 Jun 2020 17:34:35: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:34:35: #2 You may need to consider one of the other alternative d(s): 4,58 WARNING @ Sun, 21 Jun 2020 17:34:35: #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 17:34:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:34:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:34:36: 8000000 INFO @ Sun, 21 Jun 2020 17:34:39: 15000000 INFO @ Sun, 21 Jun 2020 17:34:41: 9000000 INFO @ Sun, 21 Jun 2020 17:34:44: 16000000 INFO @ Sun, 21 Jun 2020 17:34:45: 10000000 INFO @ Sun, 21 Jun 2020 17:34:49: 17000000 INFO @ Sun, 21 Jun 2020 17:34:50: 11000000 INFO @ Sun, 21 Jun 2020 17:34:53: 18000000 INFO @ Sun, 21 Jun 2020 17:34:54: 12000000 INFO @ Sun, 21 Jun 2020 17:34:58: 19000000 INFO @ Sun, 21 Jun 2020 17:34:59: 13000000 INFO @ Sun, 21 Jun 2020 17:35:03: 20000000 INFO @ Sun, 21 Jun 2020 17:35:03: 14000000 INFO @ Sun, 21 Jun 2020 17:35:03: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:35:03: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:35:03: #1 total tags in treatment: 20149421 INFO @ Sun, 21 Jun 2020 17:35:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:35:03: #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 17:35:04: #1 tags after filtering in treatment: 20149348 INFO @ Sun, 21 Jun 2020 17:35:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:35:04: #1 finished! INFO @ Sun, 21 Jun 2020 17:35:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:35:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:35:05: #2 number of paired peaks: 2360 INFO @ Sun, 21 Jun 2020 17:35:05: start model_add_line... INFO @ Sun, 21 Jun 2020 17:35:06: start X-correlation... INFO @ Sun, 21 Jun 2020 17:35:06: end of X-cor INFO @ Sun, 21 Jun 2020 17:35:06: #2 finished! INFO @ Sun, 21 Jun 2020 17:35:06: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 17:35:06: #2 alternative fragment length(s) may be 4,58 bps INFO @ Sun, 21 Jun 2020 17:35:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX089334/SRX089334.10_model.r WARNING @ Sun, 21 Jun 2020 17:35:06: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:35:06: #2 You may need to consider one of the other alternative d(s): 4,58 WARNING @ Sun, 21 Jun 2020 17:35:06: #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 17:35:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:35:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:35:08: 15000000 INFO @ Sun, 21 Jun 2020 17:35:12: 16000000 INFO @ Sun, 21 Jun 2020 17:35:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:35:17: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:35:21: 18000000 INFO @ Sun, 21 Jun 2020 17:35:26: 19000000 INFO @ Sun, 21 Jun 2020 17:35:31: 20000000 INFO @ Sun, 21 Jun 2020 17:35:31: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:35:31: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:35:31: #1 total tags in treatment: 20149421 INFO @ Sun, 21 Jun 2020 17:35:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:35:31: #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 17:35:32: #1 tags after filtering in treatment: 20149348 INFO @ Sun, 21 Jun 2020 17:35:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:35:32: #1 finished! INFO @ Sun, 21 Jun 2020 17:35:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:35:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:35:33: #2 number of paired peaks: 2360 INFO @ Sun, 21 Jun 2020 17:35:33: start model_add_line... INFO @ Sun, 21 Jun 2020 17:35:34: start X-correlation... INFO @ Sun, 21 Jun 2020 17:35:34: end of X-cor INFO @ Sun, 21 Jun 2020 17:35:34: #2 finished! INFO @ Sun, 21 Jun 2020 17:35:34: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 17:35:34: #2 alternative fragment length(s) may be 4,58 bps INFO @ Sun, 21 Jun 2020 17:35:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX089334/SRX089334.20_model.r WARNING @ Sun, 21 Jun 2020 17:35:34: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:35:34: #2 You may need to consider one of the other alternative d(s): 4,58 WARNING @ Sun, 21 Jun 2020 17:35:34: #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 17:35:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:35:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:35:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX089334/SRX089334.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:35:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX089334/SRX089334.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:35:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX089334/SRX089334.05_summits.bed INFO @ Sun, 21 Jun 2020 17:35:38: Done! pass1 - making usageList (291 chroms): 3 millis pass2 - checking and writing primary data (15619 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:35:47: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:36:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX089334/SRX089334.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:36:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX089334/SRX089334.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:36:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX089334/SRX089334.10_summits.bed INFO @ Sun, 21 Jun 2020 17:36:10: Done! pass1 - making usageList (232 chroms): 2 millis pass2 - checking and writing primary data (9716 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:36:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:36:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX089334/SRX089334.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:36:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX089334/SRX089334.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:36:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX089334/SRX089334.20_summits.bed INFO @ Sun, 21 Jun 2020 17:36:35: Done! pass1 - making usageList (175 chroms): 2 millis pass2 - checking and writing primary data (3842 records, 4 fields): 8 millis CompletedMACS2peakCalling