Job ID = 6454500 SRX = SRX2165284 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:15:54 prefetch.2.10.7: 1) Downloading 'SRR4244797'... 2020-06-21T09:15:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:19:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:19:39 prefetch.2.10.7: 1) 'SRR4244797' was downloaded successfully Read 17155473 spots for SRR4244797/SRR4244797.sra Written 17155473 spots for SRR4244797/SRR4244797.sra 2020-06-21T09:20:40 prefetch.2.10.7: 1) Downloading 'SRR4244798'... 2020-06-21T09:20:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:24:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:24:47 prefetch.2.10.7: 1) 'SRR4244798' was downloaded successfully Read 23550796 spots for SRR4244798/SRR4244798.sra Written 23550796 spots for SRR4244798/SRR4244798.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: 00:14:38 40706269 reads; of these: 40706269 (100.00%) were unpaired; of these: 4695635 (11.54%) aligned 0 times 26214811 (64.40%) aligned exactly 1 time 9795823 (24.06%) aligned >1 times 88.46% overall alignment rate Time searching: 00:14:38 Overall time: 00:14:38 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] 22516880 / 36010634 = 0.6253 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 18:47:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165284/SRX2165284.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165284/SRX2165284.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165284/SRX2165284.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165284/SRX2165284.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 18:47:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:47:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:48:05: 1000000 INFO @ Sun, 21 Jun 2020 18:48:14: 2000000 INFO @ Sun, 21 Jun 2020 18:48:22: 3000000 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 18:48:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165284/SRX2165284.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165284/SRX2165284.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165284/SRX2165284.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165284/SRX2165284.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 18:48:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:48:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:48:30: 4000000 INFO @ Sun, 21 Jun 2020 18:48:36: 1000000 INFO @ Sun, 21 Jun 2020 18:48:39: 5000000 INFO @ Sun, 21 Jun 2020 18:48:45: 2000000 INFO @ Sun, 21 Jun 2020 18:48:48: 6000000 INFO @ Sun, 21 Jun 2020 18:48:53: 3000000 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 18:48:57: 7000000 INFO @ Sun, 21 Jun 2020 18:48:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165284/SRX2165284.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165284/SRX2165284.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165284/SRX2165284.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165284/SRX2165284.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 18:48:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:48:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:49:02: 4000000 INFO @ Sun, 21 Jun 2020 18:49:06: 1000000 INFO @ Sun, 21 Jun 2020 18:49:06: 8000000 INFO @ Sun, 21 Jun 2020 18:49:11: 5000000 INFO @ Sun, 21 Jun 2020 18:49:14: 2000000 INFO @ Sun, 21 Jun 2020 18:49:15: 9000000 INFO @ Sun, 21 Jun 2020 18:49:20: 6000000 INFO @ Sun, 21 Jun 2020 18:49:23: 3000000 INFO @ Sun, 21 Jun 2020 18:49:24: 10000000 INFO @ Sun, 21 Jun 2020 18:49:29: 7000000 INFO @ Sun, 21 Jun 2020 18:49:32: 4000000 INFO @ Sun, 21 Jun 2020 18:49:33: 11000000 INFO @ Sun, 21 Jun 2020 18:49:38: 8000000 INFO @ Sun, 21 Jun 2020 18:49:41: 5000000 INFO @ Sun, 21 Jun 2020 18:49:42: 12000000 INFO @ Sun, 21 Jun 2020 18:49:47: 9000000 INFO @ Sun, 21 Jun 2020 18:49:50: 6000000 INFO @ Sun, 21 Jun 2020 18:49:51: 13000000 INFO @ Sun, 21 Jun 2020 18:49:55: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 18:49:55: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 18:49:55: #1 total tags in treatment: 13493754 INFO @ Sun, 21 Jun 2020 18:49:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:49:55: #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 18:49:55: 10000000 INFO @ Sun, 21 Jun 2020 18:49:56: #1 tags after filtering in treatment: 13493752 INFO @ Sun, 21 Jun 2020 18:49:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:49:56: #1 finished! INFO @ Sun, 21 Jun 2020 18:49:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:49:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:49:57: #2 number of paired peaks: 1053 INFO @ Sun, 21 Jun 2020 18:49:57: start model_add_line... INFO @ Sun, 21 Jun 2020 18:49:57: start X-correlation... INFO @ Sun, 21 Jun 2020 18:49:57: end of X-cor INFO @ Sun, 21 Jun 2020 18:49:57: #2 finished! INFO @ Sun, 21 Jun 2020 18:49:57: #2 predicted fragment length is 73 bps INFO @ Sun, 21 Jun 2020 18:49:57: #2 alternative fragment length(s) may be 4,73 bps INFO @ Sun, 21 Jun 2020 18:49:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165284/SRX2165284.05_model.r WARNING @ Sun, 21 Jun 2020 18:49:57: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:49:57: #2 You may need to consider one of the other alternative d(s): 4,73 WARNING @ Sun, 21 Jun 2020 18:49:57: #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 18:49:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:49:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:49:58: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:50:05: 11000000 INFO @ Sun, 21 Jun 2020 18:50:07: 8000000 INFO @ Sun, 21 Jun 2020 18:50:13: 12000000 INFO @ Sun, 21 Jun 2020 18:50:15: 9000000 INFO @ Sun, 21 Jun 2020 18:50:22: 13000000 INFO @ Sun, 21 Jun 2020 18:50:24: 10000000 INFO @ Sun, 21 Jun 2020 18:50:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:50:26: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 18:50:26: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 18:50:26: #1 total tags in treatment: 13493754 INFO @ Sun, 21 Jun 2020 18:50:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:50:26: #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 18:50:27: #1 tags after filtering in treatment: 13493752 INFO @ Sun, 21 Jun 2020 18:50:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:50:27: #1 finished! INFO @ Sun, 21 Jun 2020 18:50:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:50:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:50:28: #2 number of paired peaks: 1053 INFO @ Sun, 21 Jun 2020 18:50:28: start model_add_line... INFO @ Sun, 21 Jun 2020 18:50:28: start X-correlation... INFO @ Sun, 21 Jun 2020 18:50:28: end of X-cor INFO @ Sun, 21 Jun 2020 18:50:28: #2 finished! INFO @ Sun, 21 Jun 2020 18:50:28: #2 predicted fragment length is 73 bps INFO @ Sun, 21 Jun 2020 18:50:28: #2 alternative fragment length(s) may be 4,73 bps INFO @ Sun, 21 Jun 2020 18:50:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165284/SRX2165284.10_model.r WARNING @ Sun, 21 Jun 2020 18:50:28: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:50:28: #2 You may need to consider one of the other alternative d(s): 4,73 WARNING @ Sun, 21 Jun 2020 18:50:28: #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 18:50:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:50:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:50:32: 11000000 INFO @ Sun, 21 Jun 2020 18:50:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165284/SRX2165284.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:50:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165284/SRX2165284.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:50:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165284/SRX2165284.05_summits.bed INFO @ Sun, 21 Jun 2020 18:50:38: Done! pass1 - making usageList (829 chroms): 2 millis pass2 - checking and writing primary data (3294 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:50:40: 12000000 INFO @ Sun, 21 Jun 2020 18:50:48: 13000000 INFO @ Sun, 21 Jun 2020 18:50:52: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 18:50:52: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 18:50:52: #1 total tags in treatment: 13493754 INFO @ Sun, 21 Jun 2020 18:50:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:50:52: #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 18:50:53: #1 tags after filtering in treatment: 13493752 INFO @ Sun, 21 Jun 2020 18:50:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:50:53: #1 finished! INFO @ Sun, 21 Jun 2020 18:50:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:50:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:50:54: #2 number of paired peaks: 1053 INFO @ Sun, 21 Jun 2020 18:50:54: start model_add_line... INFO @ Sun, 21 Jun 2020 18:50:54: start X-correlation... INFO @ Sun, 21 Jun 2020 18:50:54: end of X-cor INFO @ Sun, 21 Jun 2020 18:50:54: #2 finished! INFO @ Sun, 21 Jun 2020 18:50:54: #2 predicted fragment length is 73 bps INFO @ Sun, 21 Jun 2020 18:50:54: #2 alternative fragment length(s) may be 4,73 bps INFO @ Sun, 21 Jun 2020 18:50:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165284/SRX2165284.20_model.r WARNING @ Sun, 21 Jun 2020 18:50:54: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:50:54: #2 You may need to consider one of the other alternative d(s): 4,73 WARNING @ Sun, 21 Jun 2020 18:50:54: #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 18:50:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:50:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:50:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:51:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165284/SRX2165284.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:51:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165284/SRX2165284.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:51:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165284/SRX2165284.10_summits.bed INFO @ Sun, 21 Jun 2020 18:51:07: Done! pass1 - making usageList (678 chroms): 2 millis pass2 - checking and writing primary data (2125 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:51:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:51:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165284/SRX2165284.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:51:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165284/SRX2165284.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:51:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165284/SRX2165284.20_summits.bed INFO @ Sun, 21 Jun 2020 18:51:33: Done! pass1 - making usageList (552 chroms): 1 millis pass2 - checking and writing primary data (1459 records, 4 fields): 15 millis CompletedMACS2peakCalling