Job ID = 6454496 SRX = SRX2165280 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:12:39 prefetch.2.10.7: 1) Downloading 'SRR4244789'... 2020-06-21T09:12:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:18:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:18:31 prefetch.2.10.7: 1) 'SRR4244789' was downloaded successfully Read 23652961 spots for SRR4244789/SRR4244789.sra Written 23652961 spots for SRR4244789/SRR4244789.sra 2020-06-21T09:19:53 prefetch.2.10.7: 1) Downloading 'SRR4244790'... 2020-06-21T09:19:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:23:03 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:23:03 prefetch.2.10.7: 1) 'SRR4244790' was downloaded successfully Read 22140102 spots for SRR4244790/SRR4244790.sra Written 22140102 spots for SRR4244790/SRR4244790.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: 00:13:34 45793063 reads; of these: 45793063 (100.00%) were unpaired; of these: 12267605 (26.79%) aligned 0 times 24673202 (53.88%) aligned exactly 1 time 8852256 (19.33%) aligned >1 times 73.21% overall alignment rate Time searching: 00:13:34 Overall time: 00:13:34 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] 17461977 / 33525458 = 0.5209 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 18:47:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165280/SRX2165280.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165280/SRX2165280.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165280/SRX2165280.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165280/SRX2165280.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 18:47:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:47:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:47:38: 1000000 INFO @ Sun, 21 Jun 2020 18:47:44: 2000000 INFO @ Sun, 21 Jun 2020 18:47:49: 3000000 INFO @ Sun, 21 Jun 2020 18:47:55: 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 18:48:01: 5000000 INFO @ Sun, 21 Jun 2020 18:48:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165280/SRX2165280.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165280/SRX2165280.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165280/SRX2165280.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165280/SRX2165280.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 18:48:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:48:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:48:07: 6000000 INFO @ Sun, 21 Jun 2020 18:48:08: 1000000 INFO @ Sun, 21 Jun 2020 18:48:13: 7000000 INFO @ Sun, 21 Jun 2020 18:48:14: 2000000 INFO @ Sun, 21 Jun 2020 18:48:19: 8000000 INFO @ Sun, 21 Jun 2020 18:48:21: 3000000 INFO @ Sun, 21 Jun 2020 18:48:25: 9000000 INFO @ Sun, 21 Jun 2020 18:48:27: 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 18:48:32: 10000000 INFO @ Sun, 21 Jun 2020 18:48:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165280/SRX2165280.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165280/SRX2165280.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165280/SRX2165280.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165280/SRX2165280.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 18:48:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:48:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:48:33: 5000000 INFO @ Sun, 21 Jun 2020 18:48:38: 1000000 INFO @ Sun, 21 Jun 2020 18:48:38: 11000000 INFO @ Sun, 21 Jun 2020 18:48:39: 6000000 INFO @ Sun, 21 Jun 2020 18:48:44: 2000000 INFO @ Sun, 21 Jun 2020 18:48:44: 12000000 INFO @ Sun, 21 Jun 2020 18:48:46: 7000000 INFO @ Sun, 21 Jun 2020 18:48:50: 3000000 INFO @ Sun, 21 Jun 2020 18:48:51: 13000000 INFO @ Sun, 21 Jun 2020 18:48:52: 8000000 INFO @ Sun, 21 Jun 2020 18:48:56: 4000000 INFO @ Sun, 21 Jun 2020 18:48:58: 14000000 INFO @ Sun, 21 Jun 2020 18:48:58: 9000000 INFO @ Sun, 21 Jun 2020 18:49:02: 5000000 INFO @ Sun, 21 Jun 2020 18:49:04: 15000000 INFO @ Sun, 21 Jun 2020 18:49:04: 10000000 INFO @ Sun, 21 Jun 2020 18:49:08: 6000000 INFO @ Sun, 21 Jun 2020 18:49:10: 16000000 INFO @ Sun, 21 Jun 2020 18:49:11: 11000000 INFO @ Sun, 21 Jun 2020 18:49:11: #1 tag size is determined as 67 bps INFO @ Sun, 21 Jun 2020 18:49:11: #1 tag size = 67 INFO @ Sun, 21 Jun 2020 18:49:11: #1 total tags in treatment: 16063481 INFO @ Sun, 21 Jun 2020 18:49:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:49:11: #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 18:49:11: #1 tags after filtering in treatment: 16063480 INFO @ Sun, 21 Jun 2020 18:49:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:49:11: #1 finished! INFO @ Sun, 21 Jun 2020 18:49:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:49:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:49:13: #2 number of paired peaks: 1013 INFO @ Sun, 21 Jun 2020 18:49:13: start model_add_line... INFO @ Sun, 21 Jun 2020 18:49:13: start X-correlation... INFO @ Sun, 21 Jun 2020 18:49:13: end of X-cor INFO @ Sun, 21 Jun 2020 18:49:13: #2 finished! INFO @ Sun, 21 Jun 2020 18:49:13: #2 predicted fragment length is 65 bps INFO @ Sun, 21 Jun 2020 18:49:13: #2 alternative fragment length(s) may be 3,65 bps INFO @ Sun, 21 Jun 2020 18:49:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165280/SRX2165280.05_model.r WARNING @ Sun, 21 Jun 2020 18:49:13: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:49:13: #2 You may need to consider one of the other alternative d(s): 3,65 WARNING @ Sun, 21 Jun 2020 18:49:13: #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 18:49:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:49:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:49:14: 7000000 INFO @ Sun, 21 Jun 2020 18:49:17: 12000000 INFO @ Sun, 21 Jun 2020 18:49:20: 8000000 INFO @ Sun, 21 Jun 2020 18:49:23: 13000000 INFO @ Sun, 21 Jun 2020 18:49:26: 9000000 INFO @ Sun, 21 Jun 2020 18:49:29: 14000000 INFO @ Sun, 21 Jun 2020 18:49:32: 10000000 INFO @ Sun, 21 Jun 2020 18:49:36: 15000000 INFO @ Sun, 21 Jun 2020 18:49:38: 11000000 INFO @ Sun, 21 Jun 2020 18:49:42: 16000000 INFO @ Sun, 21 Jun 2020 18:49:42: #1 tag size is determined as 67 bps INFO @ Sun, 21 Jun 2020 18:49:42: #1 tag size = 67 INFO @ Sun, 21 Jun 2020 18:49:42: #1 total tags in treatment: 16063481 INFO @ Sun, 21 Jun 2020 18:49:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:49:42: #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 18:49:43: #1 tags after filtering in treatment: 16063480 INFO @ Sun, 21 Jun 2020 18:49:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:49:43: #1 finished! INFO @ Sun, 21 Jun 2020 18:49:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:49:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:49:44: 12000000 INFO @ Sun, 21 Jun 2020 18:49:44: #2 number of paired peaks: 1013 INFO @ Sun, 21 Jun 2020 18:49:44: start model_add_line... INFO @ Sun, 21 Jun 2020 18:49:44: start X-correlation... INFO @ Sun, 21 Jun 2020 18:49:44: end of X-cor INFO @ Sun, 21 Jun 2020 18:49:44: #2 finished! INFO @ Sun, 21 Jun 2020 18:49:44: #2 predicted fragment length is 65 bps INFO @ Sun, 21 Jun 2020 18:49:44: #2 alternative fragment length(s) may be 3,65 bps INFO @ Sun, 21 Jun 2020 18:49:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165280/SRX2165280.10_model.r WARNING @ Sun, 21 Jun 2020 18:49:44: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:49:44: #2 You may need to consider one of the other alternative d(s): 3,65 WARNING @ Sun, 21 Jun 2020 18:49:44: #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 18:49:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:49:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:49:46: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:49:50: 13000000 INFO @ Sun, 21 Jun 2020 18:49:56: 14000000 INFO @ Sun, 21 Jun 2020 18:50:02: 15000000 INFO @ Sun, 21 Jun 2020 18:50:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165280/SRX2165280.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:50:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165280/SRX2165280.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:50:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165280/SRX2165280.05_summits.bed INFO @ Sun, 21 Jun 2020 18:50:02: Done! pass1 - making usageList (779 chroms): 1 millis pass2 - checking and writing primary data (3549 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:50:07: 16000000 INFO @ Sun, 21 Jun 2020 18:50:08: #1 tag size is determined as 67 bps INFO @ Sun, 21 Jun 2020 18:50:08: #1 tag size = 67 INFO @ Sun, 21 Jun 2020 18:50:08: #1 total tags in treatment: 16063481 INFO @ Sun, 21 Jun 2020 18:50:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:50:08: #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 18:50:08: #1 tags after filtering in treatment: 16063480 INFO @ Sun, 21 Jun 2020 18:50:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:50:08: #1 finished! INFO @ Sun, 21 Jun 2020 18:50:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:50:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:50:10: #2 number of paired peaks: 1013 INFO @ Sun, 21 Jun 2020 18:50:10: start model_add_line... INFO @ Sun, 21 Jun 2020 18:50:10: start X-correlation... INFO @ Sun, 21 Jun 2020 18:50:10: end of X-cor INFO @ Sun, 21 Jun 2020 18:50:10: #2 finished! INFO @ Sun, 21 Jun 2020 18:50:10: #2 predicted fragment length is 65 bps INFO @ Sun, 21 Jun 2020 18:50:10: #2 alternative fragment length(s) may be 3,65 bps INFO @ Sun, 21 Jun 2020 18:50:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165280/SRX2165280.20_model.r WARNING @ Sun, 21 Jun 2020 18:50:10: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:50:10: #2 You may need to consider one of the other alternative d(s): 3,65 WARNING @ Sun, 21 Jun 2020 18:50:10: #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 18:50:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:50:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:50:17: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:50:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165280/SRX2165280.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:50:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165280/SRX2165280.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:50:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165280/SRX2165280.10_summits.bed INFO @ Sun, 21 Jun 2020 18:50:33: Done! pass1 - making usageList (655 chroms): 1 millis pass2 - checking and writing primary data (2438 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:50:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:50:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165280/SRX2165280.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:50:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165280/SRX2165280.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:50:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165280/SRX2165280.20_summits.bed INFO @ Sun, 21 Jun 2020 18:50:58: Done! pass1 - making usageList (532 chroms): 1 millis pass2 - checking and writing primary data (1639 records, 4 fields): 17 millis CompletedMACS2peakCalling