Job ID = 6454479 SRX = SRX2165266 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:25:14 prefetch.2.10.7: 1) Downloading 'SRR4244761'... 2020-06-21T09:25:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:28:26 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:28:26 prefetch.2.10.7: 1) 'SRR4244761' was downloaded successfully Read 14835322 spots for SRR4244761/SRR4244761.sra Written 14835322 spots for SRR4244761/SRR4244761.sra 2020-06-21T09:29:21 prefetch.2.10.7: 1) Downloading 'SRR4244762'... 2020-06-21T09:29:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:33:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:33:22 prefetch.2.10.7: 1) 'SRR4244762' was downloaded successfully Read 14488212 spots for SRR4244762/SRR4244762.sra Written 14488212 spots for SRR4244762/SRR4244762.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: 00:00:01 Multiseed full-index search: 00:09:45 29323534 reads; of these: 29323534 (100.00%) were unpaired; of these: 2851639 (9.72%) aligned 0 times 19175156 (65.39%) aligned exactly 1 time 7296739 (24.88%) aligned >1 times 90.28% overall alignment rate Time searching: 00:09:46 Overall time: 00:09:46 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] 13358169 / 26471895 = 0.5046 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 18:50:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165266/SRX2165266.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165266/SRX2165266.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165266/SRX2165266.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165266/SRX2165266.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 18:50:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:50:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:50:42: 1000000 INFO @ Sun, 21 Jun 2020 18:50:47: 2000000 INFO @ Sun, 21 Jun 2020 18:50:53: 3000000 INFO @ Sun, 21 Jun 2020 18:50:58: 4000000 INFO @ Sun, 21 Jun 2020 18:51:04: 5000000 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 18:51:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165266/SRX2165266.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165266/SRX2165266.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165266/SRX2165266.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165266/SRX2165266.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 18:51:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:51:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:51:09: 6000000 INFO @ Sun, 21 Jun 2020 18:51:13: 1000000 INFO @ Sun, 21 Jun 2020 18:51:15: 7000000 INFO @ Sun, 21 Jun 2020 18:51:19: 2000000 INFO @ Sun, 21 Jun 2020 18:51:20: 8000000 INFO @ Sun, 21 Jun 2020 18:51:24: 3000000 INFO @ Sun, 21 Jun 2020 18:51:26: 9000000 INFO @ Sun, 21 Jun 2020 18:51:30: 4000000 INFO @ Sun, 21 Jun 2020 18:51:32: 10000000 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 18:51:36: 5000000 INFO @ Sun, 21 Jun 2020 18:51:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165266/SRX2165266.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165266/SRX2165266.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165266/SRX2165266.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165266/SRX2165266.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 18:51:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:51:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:51:38: 11000000 INFO @ Sun, 21 Jun 2020 18:51:42: 6000000 INFO @ Sun, 21 Jun 2020 18:51:42: 1000000 INFO @ Sun, 21 Jun 2020 18:51:43: 12000000 INFO @ Sun, 21 Jun 2020 18:51:48: 7000000 INFO @ Sun, 21 Jun 2020 18:51:48: 2000000 INFO @ Sun, 21 Jun 2020 18:51:49: 13000000 INFO @ Sun, 21 Jun 2020 18:51:50: #1 tag size is determined as 67 bps INFO @ Sun, 21 Jun 2020 18:51:50: #1 tag size = 67 INFO @ Sun, 21 Jun 2020 18:51:50: #1 total tags in treatment: 13113726 INFO @ Sun, 21 Jun 2020 18:51:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:51:50: #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 18:51:51: #1 tags after filtering in treatment: 13113716 INFO @ Sun, 21 Jun 2020 18:51:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:51:51: #1 finished! INFO @ Sun, 21 Jun 2020 18:51:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:51:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:51:52: #2 number of paired peaks: 1014 INFO @ Sun, 21 Jun 2020 18:51:52: start model_add_line... INFO @ Sun, 21 Jun 2020 18:51:52: start X-correlation... INFO @ Sun, 21 Jun 2020 18:51:52: end of X-cor INFO @ Sun, 21 Jun 2020 18:51:52: #2 finished! INFO @ Sun, 21 Jun 2020 18:51:52: #2 predicted fragment length is 62 bps INFO @ Sun, 21 Jun 2020 18:51:52: #2 alternative fragment length(s) may be 3,62 bps INFO @ Sun, 21 Jun 2020 18:51:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165266/SRX2165266.05_model.r WARNING @ Sun, 21 Jun 2020 18:51:52: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:51:52: #2 You may need to consider one of the other alternative d(s): 3,62 WARNING @ Sun, 21 Jun 2020 18:51:52: #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 18:51:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:51:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:51:53: 8000000 INFO @ Sun, 21 Jun 2020 18:51:54: 3000000 INFO @ Sun, 21 Jun 2020 18:51:59: 9000000 INFO @ Sun, 21 Jun 2020 18:52:00: 4000000 INFO @ Sun, 21 Jun 2020 18:52:05: 10000000 INFO @ Sun, 21 Jun 2020 18:52:06: 5000000 INFO @ Sun, 21 Jun 2020 18:52:11: 11000000 INFO @ Sun, 21 Jun 2020 18:52:11: 6000000 INFO @ Sun, 21 Jun 2020 18:52:17: 12000000 INFO @ Sun, 21 Jun 2020 18:52:17: 7000000 INFO @ Sun, 21 Jun 2020 18:52:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:52:23: 13000000 INFO @ Sun, 21 Jun 2020 18:52:23: 8000000 INFO @ Sun, 21 Jun 2020 18:52:24: #1 tag size is determined as 67 bps INFO @ Sun, 21 Jun 2020 18:52:24: #1 tag size = 67 INFO @ Sun, 21 Jun 2020 18:52:24: #1 total tags in treatment: 13113726 INFO @ Sun, 21 Jun 2020 18:52:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:52:24: #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 18:52:24: #1 tags after filtering in treatment: 13113716 INFO @ Sun, 21 Jun 2020 18:52:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:52:24: #1 finished! INFO @ Sun, 21 Jun 2020 18:52:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:52:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:52:25: #2 number of paired peaks: 1014 INFO @ Sun, 21 Jun 2020 18:52:25: start model_add_line... INFO @ Sun, 21 Jun 2020 18:52:25: start X-correlation... INFO @ Sun, 21 Jun 2020 18:52:25: end of X-cor INFO @ Sun, 21 Jun 2020 18:52:25: #2 finished! INFO @ Sun, 21 Jun 2020 18:52:25: #2 predicted fragment length is 62 bps INFO @ Sun, 21 Jun 2020 18:52:25: #2 alternative fragment length(s) may be 3,62 bps INFO @ Sun, 21 Jun 2020 18:52:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165266/SRX2165266.10_model.r WARNING @ Sun, 21 Jun 2020 18:52:25: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:52:25: #2 You may need to consider one of the other alternative d(s): 3,62 WARNING @ Sun, 21 Jun 2020 18:52:25: #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 18:52:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:52:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:52:28: 9000000 INFO @ Sun, 21 Jun 2020 18:52:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165266/SRX2165266.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:52:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165266/SRX2165266.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:52:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165266/SRX2165266.05_summits.bed INFO @ Sun, 21 Jun 2020 18:52:32: Done! pass1 - making usageList (767 chroms): 2 millis pass2 - checking and writing primary data (3203 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:52:34: 10000000 INFO @ Sun, 21 Jun 2020 18:52:40: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:52:45: 12000000 INFO @ Sun, 21 Jun 2020 18:52:51: 13000000 INFO @ Sun, 21 Jun 2020 18:52:52: #1 tag size is determined as 67 bps INFO @ Sun, 21 Jun 2020 18:52:52: #1 tag size = 67 INFO @ Sun, 21 Jun 2020 18:52:52: #1 total tags in treatment: 13113726 INFO @ Sun, 21 Jun 2020 18:52:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:52:52: #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 18:52:52: #1 tags after filtering in treatment: 13113716 INFO @ Sun, 21 Jun 2020 18:52:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:52:52: #1 finished! INFO @ Sun, 21 Jun 2020 18:52:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:52:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:52:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:52:53: #2 number of paired peaks: 1014 INFO @ Sun, 21 Jun 2020 18:52:53: start model_add_line... INFO @ Sun, 21 Jun 2020 18:52:53: start X-correlation... INFO @ Sun, 21 Jun 2020 18:52:53: end of X-cor INFO @ Sun, 21 Jun 2020 18:52:53: #2 finished! INFO @ Sun, 21 Jun 2020 18:52:53: #2 predicted fragment length is 62 bps INFO @ Sun, 21 Jun 2020 18:52:53: #2 alternative fragment length(s) may be 3,62 bps INFO @ Sun, 21 Jun 2020 18:52:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165266/SRX2165266.20_model.r WARNING @ Sun, 21 Jun 2020 18:52:53: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:52:53: #2 You may need to consider one of the other alternative d(s): 3,62 WARNING @ Sun, 21 Jun 2020 18:52:53: #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 18:52:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:52:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:53:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165266/SRX2165266.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:53:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165266/SRX2165266.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:53:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165266/SRX2165266.10_summits.bed INFO @ Sun, 21 Jun 2020 18:53:06: Done! pass1 - making usageList (638 chroms): 2 millis pass2 - checking and writing primary data (2155 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:53:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:53:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165266/SRX2165266.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:53:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165266/SRX2165266.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:53:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165266/SRX2165266.20_summits.bed INFO @ Sun, 21 Jun 2020 18:53:34: Done! pass1 - making usageList (510 chroms): 2 millis pass2 - checking and writing primary data (1448 records, 4 fields): 16 millis CompletedMACS2peakCalling