Job ID = 6498031 SRX = SRX287904 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:13:18 prefetch.2.10.7: 1) Downloading 'SRR870093'... 2020-06-25T23:13:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:15:26 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:15:26 prefetch.2.10.7: 1) 'SRR870093' was downloaded successfully Read 16839930 spots for SRR870093/SRR870093.sra Written 16839930 spots for SRR870093/SRR870093.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: 00:06:35 16839930 reads; of these: 16839930 (100.00%) were unpaired; of these: 930880 (5.53%) aligned 0 times 11638439 (69.11%) aligned exactly 1 time 4270611 (25.36%) aligned >1 times 94.47% overall alignment rate Time searching: 00:06:35 Overall time: 00:06:35 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1513392 / 15909050 = 0.0951 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 @ Fri, 26 Jun 2020 08:27:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287904/SRX287904.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287904/SRX287904.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287904/SRX287904.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287904/SRX287904.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 @ Fri, 26 Jun 2020 08:27:31: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:27:31: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:27:37: 1000000 INFO @ Fri, 26 Jun 2020 08:27:43: 2000000 INFO @ Fri, 26 Jun 2020 08:27:49: 3000000 INFO @ Fri, 26 Jun 2020 08:27:55: 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 @ Fri, 26 Jun 2020 08:28:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287904/SRX287904.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287904/SRX287904.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287904/SRX287904.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287904/SRX287904.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 @ Fri, 26 Jun 2020 08:28:01: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:28:01: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:28:02: 5000000 INFO @ Fri, 26 Jun 2020 08:28:08: 1000000 INFO @ Fri, 26 Jun 2020 08:28:08: 6000000 INFO @ Fri, 26 Jun 2020 08:28:14: 2000000 INFO @ Fri, 26 Jun 2020 08:28:14: 7000000 INFO @ Fri, 26 Jun 2020 08:28:21: 8000000 INFO @ Fri, 26 Jun 2020 08:28:21: 3000000 INFO @ Fri, 26 Jun 2020 08:28:27: 9000000 INFO @ Fri, 26 Jun 2020 08:28:27: 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 @ Fri, 26 Jun 2020 08:28:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287904/SRX287904.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287904/SRX287904.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287904/SRX287904.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287904/SRX287904.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 @ Fri, 26 Jun 2020 08:28:31: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:28:31: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:28:34: 10000000 INFO @ Fri, 26 Jun 2020 08:28:34: 5000000 INFO @ Fri, 26 Jun 2020 08:28:38: 1000000 INFO @ Fri, 26 Jun 2020 08:28:41: 11000000 INFO @ Fri, 26 Jun 2020 08:28:41: 6000000 INFO @ Fri, 26 Jun 2020 08:28:45: 2000000 INFO @ Fri, 26 Jun 2020 08:28:48: 7000000 INFO @ Fri, 26 Jun 2020 08:28:48: 12000000 INFO @ Fri, 26 Jun 2020 08:28:52: 3000000 INFO @ Fri, 26 Jun 2020 08:28:55: 8000000 INFO @ Fri, 26 Jun 2020 08:28:55: 13000000 INFO @ Fri, 26 Jun 2020 08:28:58: 4000000 INFO @ Fri, 26 Jun 2020 08:29:01: 9000000 INFO @ Fri, 26 Jun 2020 08:29:02: 14000000 INFO @ Fri, 26 Jun 2020 08:29:04: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:29:04: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:29:04: #1 total tags in treatment: 14395658 INFO @ Fri, 26 Jun 2020 08:29:04: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:29:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:29:05: #1 tags after filtering in treatment: 14395658 INFO @ Fri, 26 Jun 2020 08:29:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:29:05: #1 finished! INFO @ Fri, 26 Jun 2020 08:29:05: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:29:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:29:05: 5000000 INFO @ Fri, 26 Jun 2020 08:29:06: #2 number of paired peaks: 202 WARNING @ Fri, 26 Jun 2020 08:29:06: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Fri, 26 Jun 2020 08:29:06: start model_add_line... INFO @ Fri, 26 Jun 2020 08:29:06: start X-correlation... INFO @ Fri, 26 Jun 2020 08:29:06: end of X-cor INFO @ Fri, 26 Jun 2020 08:29:06: #2 finished! INFO @ Fri, 26 Jun 2020 08:29:06: #2 predicted fragment length is 122 bps INFO @ Fri, 26 Jun 2020 08:29:06: #2 alternative fragment length(s) may be 122 bps INFO @ Fri, 26 Jun 2020 08:29:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287904/SRX287904.05_model.r INFO @ Fri, 26 Jun 2020 08:29:06: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:29:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:29:08: 10000000 INFO @ Fri, 26 Jun 2020 08:29:12: 6000000 INFO @ Fri, 26 Jun 2020 08:29:15: 11000000 INFO @ Fri, 26 Jun 2020 08:29:18: 7000000 INFO @ Fri, 26 Jun 2020 08:29:22: 12000000 INFO @ Fri, 26 Jun 2020 08:29:25: 8000000 INFO @ Fri, 26 Jun 2020 08:29:29: 13000000 INFO @ Fri, 26 Jun 2020 08:29:31: 9000000 INFO @ Fri, 26 Jun 2020 08:29:36: 14000000 INFO @ Fri, 26 Jun 2020 08:29:38: 10000000 INFO @ Fri, 26 Jun 2020 08:29:38: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:29:38: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:29:38: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:29:38: #1 total tags in treatment: 14395658 INFO @ Fri, 26 Jun 2020 08:29:38: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:29:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:29:38: #1 tags after filtering in treatment: 14395658 INFO @ Fri, 26 Jun 2020 08:29:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:29:38: #1 finished! INFO @ Fri, 26 Jun 2020 08:29:38: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:29:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:29:40: #2 number of paired peaks: 202 WARNING @ Fri, 26 Jun 2020 08:29:40: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Fri, 26 Jun 2020 08:29:40: start model_add_line... INFO @ Fri, 26 Jun 2020 08:29:40: start X-correlation... INFO @ Fri, 26 Jun 2020 08:29:40: end of X-cor INFO @ Fri, 26 Jun 2020 08:29:40: #2 finished! INFO @ Fri, 26 Jun 2020 08:29:40: #2 predicted fragment length is 122 bps INFO @ Fri, 26 Jun 2020 08:29:40: #2 alternative fragment length(s) may be 122 bps INFO @ Fri, 26 Jun 2020 08:29:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287904/SRX287904.10_model.r INFO @ Fri, 26 Jun 2020 08:29:40: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:29:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:29:44: 11000000 INFO @ Fri, 26 Jun 2020 08:29:51: 12000000 INFO @ Fri, 26 Jun 2020 08:29:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287904/SRX287904.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:29:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287904/SRX287904.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:29:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287904/SRX287904.05_summits.bed INFO @ Fri, 26 Jun 2020 08:29:55: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4830 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:29:57: 13000000 INFO @ Fri, 26 Jun 2020 08:30:03: 14000000 INFO @ Fri, 26 Jun 2020 08:30:06: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:30:06: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:30:06: #1 total tags in treatment: 14395658 INFO @ Fri, 26 Jun 2020 08:30:06: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:30:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:30:06: #1 tags after filtering in treatment: 14395658 INFO @ Fri, 26 Jun 2020 08:30:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:30:06: #1 finished! INFO @ Fri, 26 Jun 2020 08:30:06: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:30:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:30:07: #2 number of paired peaks: 202 WARNING @ Fri, 26 Jun 2020 08:30:07: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Fri, 26 Jun 2020 08:30:07: start model_add_line... INFO @ Fri, 26 Jun 2020 08:30:07: start X-correlation... INFO @ Fri, 26 Jun 2020 08:30:07: end of X-cor INFO @ Fri, 26 Jun 2020 08:30:07: #2 finished! INFO @ Fri, 26 Jun 2020 08:30:07: #2 predicted fragment length is 122 bps INFO @ Fri, 26 Jun 2020 08:30:07: #2 alternative fragment length(s) may be 122 bps INFO @ Fri, 26 Jun 2020 08:30:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287904/SRX287904.20_model.r INFO @ Fri, 26 Jun 2020 08:30:07: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:30:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:30:14: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:30:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287904/SRX287904.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:30:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287904/SRX287904.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:30:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287904/SRX287904.10_summits.bed INFO @ Fri, 26 Jun 2020 08:30:30: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3415 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:30:40: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:30:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287904/SRX287904.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:30:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287904/SRX287904.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:30:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287904/SRX287904.20_summits.bed INFO @ Fri, 26 Jun 2020 08:30:56: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2066 records, 4 fields): 4 millis CompletedMACS2peakCalling