Job ID = 6454769 SRX = SRX2583182 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:29:44 prefetch.2.10.7: 1) Downloading 'SRR5279382'... 2020-06-21T09:29:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:33:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:33:43 prefetch.2.10.7: 'SRR5279382' is valid 2020-06-21T09:33:43 prefetch.2.10.7: 1) 'SRR5279382' was downloaded successfully 2020-06-21T09:33:43 prefetch.2.10.7: 'SRR5279382' has 0 unresolved dependencies Read 21888039 spots for SRR5279382/SRR5279382.sra Written 21888039 spots for SRR5279382/SRR5279382.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: 00:05:49 21888039 reads; of these: 21888039 (100.00%) were unpaired; of these: 1153174 (5.27%) aligned 0 times 16159828 (73.83%) aligned exactly 1 time 4575037 (20.90%) aligned >1 times 94.73% overall alignment rate Time searching: 00:05:50 Overall time: 00:05:50 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] 5231622 / 20734865 = 0.2523 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 18:46:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2583182/SRX2583182.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2583182/SRX2583182.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2583182/SRX2583182.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2583182/SRX2583182.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 18:46:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:46:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:46:44: 1000000 INFO @ Sun, 21 Jun 2020 18:46:49: 2000000 INFO @ Sun, 21 Jun 2020 18:46:53: 3000000 INFO @ Sun, 21 Jun 2020 18:46:58: 4000000 INFO @ Sun, 21 Jun 2020 18:47:03: 5000000 INFO @ Sun, 21 Jun 2020 18:47:07: 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 18:47:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2583182/SRX2583182.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2583182/SRX2583182.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2583182/SRX2583182.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2583182/SRX2583182.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 18:47:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:47:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:47:12: 7000000 INFO @ Sun, 21 Jun 2020 18:47:14: 1000000 INFO @ Sun, 21 Jun 2020 18:47:16: 8000000 INFO @ Sun, 21 Jun 2020 18:47:19: 2000000 INFO @ Sun, 21 Jun 2020 18:47:21: 9000000 INFO @ Sun, 21 Jun 2020 18:47:24: 3000000 INFO @ Sun, 21 Jun 2020 18:47:25: 10000000 INFO @ Sun, 21 Jun 2020 18:47:28: 4000000 INFO @ Sun, 21 Jun 2020 18:47:30: 11000000 INFO @ Sun, 21 Jun 2020 18:47:33: 5000000 INFO @ Sun, 21 Jun 2020 18:47:34: 12000000 INFO @ Sun, 21 Jun 2020 18:47:37: 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 18:47:39: 13000000 INFO @ Sun, 21 Jun 2020 18:47:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2583182/SRX2583182.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2583182/SRX2583182.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2583182/SRX2583182.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2583182/SRX2583182.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 18:47:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:47:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:47:42: 7000000 INFO @ Sun, 21 Jun 2020 18:47:44: 14000000 INFO @ Sun, 21 Jun 2020 18:47:44: 1000000 INFO @ Sun, 21 Jun 2020 18:47:46: 8000000 INFO @ Sun, 21 Jun 2020 18:47:49: 15000000 INFO @ Sun, 21 Jun 2020 18:47:49: 2000000 INFO @ Sun, 21 Jun 2020 18:47:51: 9000000 INFO @ Sun, 21 Jun 2020 18:47:52: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:47:52: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:47:52: #1 total tags in treatment: 15503243 INFO @ Sun, 21 Jun 2020 18:47:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:47:52: #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 18:47:52: #1 tags after filtering in treatment: 15503119 INFO @ Sun, 21 Jun 2020 18:47:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:47:52: #1 finished! INFO @ Sun, 21 Jun 2020 18:47:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:47:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:47:53: #2 number of paired peaks: 1211 INFO @ Sun, 21 Jun 2020 18:47:53: start model_add_line... INFO @ Sun, 21 Jun 2020 18:47:53: start X-correlation... INFO @ Sun, 21 Jun 2020 18:47:53: end of X-cor INFO @ Sun, 21 Jun 2020 18:47:53: #2 finished! INFO @ Sun, 21 Jun 2020 18:47:53: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 18:47:53: #2 alternative fragment length(s) may be 2,55 bps INFO @ Sun, 21 Jun 2020 18:47:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2583182/SRX2583182.05_model.r WARNING @ Sun, 21 Jun 2020 18:47:53: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:47:53: #2 You may need to consider one of the other alternative d(s): 2,55 WARNING @ Sun, 21 Jun 2020 18:47:53: #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 18:47:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:47:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:47:54: 3000000 INFO @ Sun, 21 Jun 2020 18:47:55: 10000000 INFO @ Sun, 21 Jun 2020 18:47:58: 4000000 INFO @ Sun, 21 Jun 2020 18:48:00: 11000000 INFO @ Sun, 21 Jun 2020 18:48:03: 5000000 INFO @ Sun, 21 Jun 2020 18:48:04: 12000000 INFO @ Sun, 21 Jun 2020 18:48:07: 6000000 INFO @ Sun, 21 Jun 2020 18:48:09: 13000000 INFO @ Sun, 21 Jun 2020 18:48:12: 7000000 INFO @ Sun, 21 Jun 2020 18:48:14: 14000000 INFO @ Sun, 21 Jun 2020 18:48:16: 8000000 INFO @ Sun, 21 Jun 2020 18:48:18: 15000000 INFO @ Sun, 21 Jun 2020 18:48:21: 9000000 INFO @ Sun, 21 Jun 2020 18:48:21: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:48:21: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:48:21: #1 total tags in treatment: 15503243 INFO @ Sun, 21 Jun 2020 18:48:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:48:21: #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 18:48:21: #1 tags after filtering in treatment: 15503119 INFO @ Sun, 21 Jun 2020 18:48:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:48:21: #1 finished! INFO @ Sun, 21 Jun 2020 18:48:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:48:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:48:23: #2 number of paired peaks: 1211 INFO @ Sun, 21 Jun 2020 18:48:23: start model_add_line... INFO @ Sun, 21 Jun 2020 18:48:23: start X-correlation... INFO @ Sun, 21 Jun 2020 18:48:23: end of X-cor INFO @ Sun, 21 Jun 2020 18:48:23: #2 finished! INFO @ Sun, 21 Jun 2020 18:48:23: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 18:48:23: #2 alternative fragment length(s) may be 2,55 bps INFO @ Sun, 21 Jun 2020 18:48:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2583182/SRX2583182.10_model.r WARNING @ Sun, 21 Jun 2020 18:48:23: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:48:23: #2 You may need to consider one of the other alternative d(s): 2,55 WARNING @ Sun, 21 Jun 2020 18:48:23: #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 18:48:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:48:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:48:25: 10000000 INFO @ Sun, 21 Jun 2020 18:48:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:48:30: 11000000 INFO @ Sun, 21 Jun 2020 18:48:35: 12000000 INFO @ Sun, 21 Jun 2020 18:48:39: 13000000 INFO @ Sun, 21 Jun 2020 18:48:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2583182/SRX2583182.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:48:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2583182/SRX2583182.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:48:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2583182/SRX2583182.05_summits.bed INFO @ Sun, 21 Jun 2020 18:48:42: Done! pass1 - making usageList (287 chroms): 1 millis pass2 - checking and writing primary data (2344 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:48:44: 14000000 INFO @ Sun, 21 Jun 2020 18:48:49: 15000000 INFO @ Sun, 21 Jun 2020 18:48:51: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:48:51: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:48:51: #1 total tags in treatment: 15503243 INFO @ Sun, 21 Jun 2020 18:48:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:48:51: #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 18:48:52: #1 tags after filtering in treatment: 15503119 INFO @ Sun, 21 Jun 2020 18:48:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:48:52: #1 finished! INFO @ Sun, 21 Jun 2020 18:48:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:48:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:48:53: #2 number of paired peaks: 1211 INFO @ Sun, 21 Jun 2020 18:48:53: start model_add_line... INFO @ Sun, 21 Jun 2020 18:48:53: start X-correlation... INFO @ Sun, 21 Jun 2020 18:48:53: end of X-cor INFO @ Sun, 21 Jun 2020 18:48:53: #2 finished! INFO @ Sun, 21 Jun 2020 18:48:53: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 18:48:53: #2 alternative fragment length(s) may be 2,55 bps INFO @ Sun, 21 Jun 2020 18:48:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2583182/SRX2583182.20_model.r WARNING @ Sun, 21 Jun 2020 18:48:53: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:48:53: #2 You may need to consider one of the other alternative d(s): 2,55 WARNING @ Sun, 21 Jun 2020 18:48:53: #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 18:48:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:48:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:48:54: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:49:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2583182/SRX2583182.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:49:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2583182/SRX2583182.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:49:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2583182/SRX2583182.10_summits.bed INFO @ Sun, 21 Jun 2020 18:49:10: Done! pass1 - making usageList (206 chroms): 1 millis pass2 - checking and writing primary data (1079 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:49:24: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:49:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2583182/SRX2583182.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:49:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2583182/SRX2583182.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:49:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2583182/SRX2583182.20_summits.bed INFO @ Sun, 21 Jun 2020 18:49:40: Done! pass1 - making usageList (138 chroms): 1 millis pass2 - checking and writing primary data (403 records, 4 fields): 5 millis CompletedMACS2peakCalling