Job ID = 6456525 SRX = SRX3630324 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:59:31 prefetch.2.10.7: 1) Downloading 'SRR6652846'... 2020-06-21T10:59:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:04:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:04:44 prefetch.2.10.7: 1) 'SRR6652846' was downloaded successfully 2020-06-21T11:04:44 prefetch.2.10.7: 'SRR6652846' has 0 unresolved dependencies Read 43396095 spots for SRR6652846/SRR6652846.sra Written 43396095 spots for SRR6652846/SRR6652846.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: 00:16:11 43396095 reads; of these: 43396095 (100.00%) were unpaired; of these: 1547128 (3.57%) aligned 0 times 11707249 (26.98%) aligned exactly 1 time 30141718 (69.46%) aligned >1 times 96.43% overall alignment rate Time searching: 00:16:11 Overall time: 00:16:11 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 20 files... [bam_rmdupse_core] 26790238 / 41848967 = 0.6402 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 20:30:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3630324/SRX3630324.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3630324/SRX3630324.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3630324/SRX3630324.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3630324/SRX3630324.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 20:30:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:30:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:30:54: 1000000 INFO @ Sun, 21 Jun 2020 20:30:59: 2000000 INFO @ Sun, 21 Jun 2020 20:31:04: 3000000 INFO @ Sun, 21 Jun 2020 20:31:09: 4000000 INFO @ Sun, 21 Jun 2020 20:31:14: 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 20:31:19: 6000000 INFO @ Sun, 21 Jun 2020 20:31:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3630324/SRX3630324.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3630324/SRX3630324.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3630324/SRX3630324.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3630324/SRX3630324.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 20:31:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:31:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:31:24: 7000000 INFO @ Sun, 21 Jun 2020 20:31:24: 1000000 INFO @ Sun, 21 Jun 2020 20:31:29: 8000000 INFO @ Sun, 21 Jun 2020 20:31:29: 2000000 INFO @ Sun, 21 Jun 2020 20:31:33: 3000000 INFO @ Sun, 21 Jun 2020 20:31:33: 9000000 INFO @ Sun, 21 Jun 2020 20:31:38: 4000000 INFO @ Sun, 21 Jun 2020 20:31:38: 10000000 INFO @ Sun, 21 Jun 2020 20:31:43: 5000000 INFO @ Sun, 21 Jun 2020 20:31:44: 11000000 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 20:31:48: 6000000 INFO @ Sun, 21 Jun 2020 20:31:49: 12000000 INFO @ Sun, 21 Jun 2020 20:31:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3630324/SRX3630324.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3630324/SRX3630324.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3630324/SRX3630324.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3630324/SRX3630324.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 20:31:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:31:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:31:53: 7000000 INFO @ Sun, 21 Jun 2020 20:31:54: 13000000 INFO @ Sun, 21 Jun 2020 20:31:54: 1000000 INFO @ Sun, 21 Jun 2020 20:31:57: 8000000 INFO @ Sun, 21 Jun 2020 20:31:59: 14000000 INFO @ Sun, 21 Jun 2020 20:31:59: 2000000 INFO @ Sun, 21 Jun 2020 20:32:02: 9000000 INFO @ Sun, 21 Jun 2020 20:32:04: 15000000 INFO @ Sun, 21 Jun 2020 20:32:04: 3000000 INFO @ Sun, 21 Jun 2020 20:32:04: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:32:04: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:32:04: #1 total tags in treatment: 15058729 INFO @ Sun, 21 Jun 2020 20:32:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:32:04: #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 20:32:05: #1 tags after filtering in treatment: 15058695 INFO @ Sun, 21 Jun 2020 20:32:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:32:05: #1 finished! INFO @ Sun, 21 Jun 2020 20:32:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:32:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:32:07: #2 number of paired peaks: 10786 INFO @ Sun, 21 Jun 2020 20:32:07: start model_add_line... INFO @ Sun, 21 Jun 2020 20:32:07: start X-correlation... INFO @ Sun, 21 Jun 2020 20:32:07: end of X-cor INFO @ Sun, 21 Jun 2020 20:32:07: #2 finished! INFO @ Sun, 21 Jun 2020 20:32:07: #2 predicted fragment length is 102 bps INFO @ Sun, 21 Jun 2020 20:32:07: #2 alternative fragment length(s) may be 3,102 bps INFO @ Sun, 21 Jun 2020 20:32:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3630324/SRX3630324.05_model.r WARNING @ Sun, 21 Jun 2020 20:32:07: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:32:07: #2 You may need to consider one of the other alternative d(s): 3,102 WARNING @ Sun, 21 Jun 2020 20:32:07: #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 20:32:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:32:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:32:07: 10000000 INFO @ Sun, 21 Jun 2020 20:32:09: 4000000 INFO @ Sun, 21 Jun 2020 20:32:12: 11000000 INFO @ Sun, 21 Jun 2020 20:32:14: 5000000 INFO @ Sun, 21 Jun 2020 20:32:17: 12000000 INFO @ Sun, 21 Jun 2020 20:32:18: 6000000 INFO @ Sun, 21 Jun 2020 20:32:22: 13000000 INFO @ Sun, 21 Jun 2020 20:32:23: 7000000 INFO @ Sun, 21 Jun 2020 20:32:27: 14000000 INFO @ Sun, 21 Jun 2020 20:32:28: 8000000 INFO @ Sun, 21 Jun 2020 20:32:32: 15000000 INFO @ Sun, 21 Jun 2020 20:32:32: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:32:32: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:32:32: #1 total tags in treatment: 15058729 INFO @ Sun, 21 Jun 2020 20:32:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:32:32: #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 20:32:33: 9000000 INFO @ Sun, 21 Jun 2020 20:32:33: #1 tags after filtering in treatment: 15058695 INFO @ Sun, 21 Jun 2020 20:32:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:32:33: #1 finished! INFO @ Sun, 21 Jun 2020 20:32:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:32:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:32:35: #2 number of paired peaks: 10786 INFO @ Sun, 21 Jun 2020 20:32:35: start model_add_line... INFO @ Sun, 21 Jun 2020 20:32:35: start X-correlation... INFO @ Sun, 21 Jun 2020 20:32:35: end of X-cor INFO @ Sun, 21 Jun 2020 20:32:35: #2 finished! INFO @ Sun, 21 Jun 2020 20:32:35: #2 predicted fragment length is 102 bps INFO @ Sun, 21 Jun 2020 20:32:35: #2 alternative fragment length(s) may be 3,102 bps INFO @ Sun, 21 Jun 2020 20:32:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3630324/SRX3630324.10_model.r WARNING @ Sun, 21 Jun 2020 20:32:35: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:32:35: #2 You may need to consider one of the other alternative d(s): 3,102 WARNING @ Sun, 21 Jun 2020 20:32:35: #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 20:32:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:32:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:32:37: 10000000 INFO @ Sun, 21 Jun 2020 20:32:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:32:42: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:32:47: 12000000 INFO @ Sun, 21 Jun 2020 20:32:51: 13000000 INFO @ Sun, 21 Jun 2020 20:32:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3630324/SRX3630324.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:32:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3630324/SRX3630324.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:32:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3630324/SRX3630324.05_summits.bed INFO @ Sun, 21 Jun 2020 20:32:55: Done! pass1 - making usageList (1298 chroms): 3 millis pass2 - checking and writing primary data (11592 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:32:56: 14000000 INFO @ Sun, 21 Jun 2020 20:33:01: 15000000 INFO @ Sun, 21 Jun 2020 20:33:01: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:33:01: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:33:01: #1 total tags in treatment: 15058729 INFO @ Sun, 21 Jun 2020 20:33:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:33:01: #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 20:33:02: #1 tags after filtering in treatment: 15058695 INFO @ Sun, 21 Jun 2020 20:33:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:33:02: #1 finished! INFO @ Sun, 21 Jun 2020 20:33:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:33:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:33:04: #2 number of paired peaks: 10786 INFO @ Sun, 21 Jun 2020 20:33:04: start model_add_line... INFO @ Sun, 21 Jun 2020 20:33:04: start X-correlation... INFO @ Sun, 21 Jun 2020 20:33:04: end of X-cor INFO @ Sun, 21 Jun 2020 20:33:04: #2 finished! INFO @ Sun, 21 Jun 2020 20:33:04: #2 predicted fragment length is 102 bps INFO @ Sun, 21 Jun 2020 20:33:04: #2 alternative fragment length(s) may be 3,102 bps INFO @ Sun, 21 Jun 2020 20:33:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3630324/SRX3630324.20_model.r WARNING @ Sun, 21 Jun 2020 20:33:04: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:33:04: #2 You may need to consider one of the other alternative d(s): 3,102 WARNING @ Sun, 21 Jun 2020 20:33:04: #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 20:33:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:33:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:33:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:33:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3630324/SRX3630324.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:33:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3630324/SRX3630324.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:33:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3630324/SRX3630324.10_summits.bed INFO @ Sun, 21 Jun 2020 20:33:23: Done! pass1 - making usageList (1166 chroms): 2 millis pass2 - checking and writing primary data (6967 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:33:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:33:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3630324/SRX3630324.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:33:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3630324/SRX3630324.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:33:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3630324/SRX3630324.20_summits.bed INFO @ Sun, 21 Jun 2020 20:33:51: Done! pass1 - making usageList (1013 chroms): 2 millis pass2 - checking and writing primary data (3352 records, 4 fields): 27 millis CompletedMACS2peakCalling