Job ID = 6498290 SRX = SRX467102 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:28:02 prefetch.2.10.7: 1) Downloading 'SRR1164526'... 2020-06-25T23:28:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:31:09 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:31:09 prefetch.2.10.7: 1) 'SRR1164526' was downloaded successfully Read 19299032 spots for SRR1164526/SRR1164526.sra Written 19299032 spots for SRR1164526/SRR1164526.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: 00:05:39 19299032 reads; of these: 19299032 (100.00%) were unpaired; of these: 3371334 (17.47%) aligned 0 times 12521005 (64.88%) aligned exactly 1 time 3406693 (17.65%) aligned >1 times 82.53% overall alignment rate Time searching: 00:05:39 Overall time: 00:05:39 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] 2113518 / 15927698 = 0.1327 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 08:42:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467102/SRX467102.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467102/SRX467102.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467102/SRX467102.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467102/SRX467102.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 08:42:29: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:42:29: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:42:37: 1000000 INFO @ Fri, 26 Jun 2020 08:42:44: 2000000 INFO @ Fri, 26 Jun 2020 08:42:51: 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 @ Fri, 26 Jun 2020 08:42:59: 4000000 INFO @ Fri, 26 Jun 2020 08:42:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467102/SRX467102.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467102/SRX467102.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467102/SRX467102.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467102/SRX467102.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 08:42:59: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:42:59: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:43:07: 5000000 INFO @ Fri, 26 Jun 2020 08:43:07: 1000000 INFO @ Fri, 26 Jun 2020 08:43:14: 2000000 INFO @ Fri, 26 Jun 2020 08:43:14: 6000000 INFO @ Fri, 26 Jun 2020 08:43:21: 3000000 INFO @ Fri, 26 Jun 2020 08:43:22: 7000000 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 08:43:29: 4000000 INFO @ Fri, 26 Jun 2020 08:43:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467102/SRX467102.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467102/SRX467102.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467102/SRX467102.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467102/SRX467102.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 08:43:30: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:43:30: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:43:30: 8000000 INFO @ Fri, 26 Jun 2020 08:43:36: 5000000 INFO @ Fri, 26 Jun 2020 08:43:37: 1000000 INFO @ Fri, 26 Jun 2020 08:43:38: 9000000 INFO @ Fri, 26 Jun 2020 08:43:43: 6000000 INFO @ Fri, 26 Jun 2020 08:43:44: 2000000 INFO @ Fri, 26 Jun 2020 08:43:46: 10000000 INFO @ Fri, 26 Jun 2020 08:43:51: 3000000 INFO @ Fri, 26 Jun 2020 08:43:51: 7000000 INFO @ Fri, 26 Jun 2020 08:43:54: 11000000 INFO @ Fri, 26 Jun 2020 08:43:57: 4000000 INFO @ Fri, 26 Jun 2020 08:43:58: 8000000 INFO @ Fri, 26 Jun 2020 08:44:02: 12000000 INFO @ Fri, 26 Jun 2020 08:44:04: 5000000 INFO @ Fri, 26 Jun 2020 08:44:05: 9000000 INFO @ Fri, 26 Jun 2020 08:44:10: 13000000 INFO @ Fri, 26 Jun 2020 08:44:12: 6000000 INFO @ Fri, 26 Jun 2020 08:44:12: 10000000 INFO @ Fri, 26 Jun 2020 08:44:16: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:44:16: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:44:16: #1 total tags in treatment: 13814180 INFO @ Fri, 26 Jun 2020 08:44:16: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:44:16: #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 08:44:16: #1 tags after filtering in treatment: 13814180 INFO @ Fri, 26 Jun 2020 08:44:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:44:16: #1 finished! INFO @ Fri, 26 Jun 2020 08:44:16: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:44:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:44:17: #2 number of paired peaks: 360 WARNING @ Fri, 26 Jun 2020 08:44:17: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Fri, 26 Jun 2020 08:44:17: start model_add_line... INFO @ Fri, 26 Jun 2020 08:44:17: start X-correlation... INFO @ Fri, 26 Jun 2020 08:44:17: end of X-cor INFO @ Fri, 26 Jun 2020 08:44:17: #2 finished! INFO @ Fri, 26 Jun 2020 08:44:17: #2 predicted fragment length is 166 bps INFO @ Fri, 26 Jun 2020 08:44:17: #2 alternative fragment length(s) may be 166 bps INFO @ Fri, 26 Jun 2020 08:44:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467102/SRX467102.05_model.r INFO @ Fri, 26 Jun 2020 08:44:17: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:44:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:44:18: 7000000 INFO @ Fri, 26 Jun 2020 08:44:19: 11000000 INFO @ Fri, 26 Jun 2020 08:44:25: 8000000 INFO @ Fri, 26 Jun 2020 08:44:26: 12000000 INFO @ Fri, 26 Jun 2020 08:44:32: 9000000 INFO @ Fri, 26 Jun 2020 08:44:33: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:44:38: 10000000 INFO @ Fri, 26 Jun 2020 08:44:38: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:44:38: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:44:38: #1 total tags in treatment: 13814180 INFO @ Fri, 26 Jun 2020 08:44:38: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:44:38: #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 08:44:38: #1 tags after filtering in treatment: 13814180 INFO @ Fri, 26 Jun 2020 08:44:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:44:38: #1 finished! INFO @ Fri, 26 Jun 2020 08:44:38: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:44:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:44:39: #2 number of paired peaks: 360 WARNING @ Fri, 26 Jun 2020 08:44:39: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Fri, 26 Jun 2020 08:44:39: start model_add_line... INFO @ Fri, 26 Jun 2020 08:44:39: start X-correlation... INFO @ Fri, 26 Jun 2020 08:44:40: end of X-cor INFO @ Fri, 26 Jun 2020 08:44:40: #2 finished! INFO @ Fri, 26 Jun 2020 08:44:40: #2 predicted fragment length is 166 bps INFO @ Fri, 26 Jun 2020 08:44:40: #2 alternative fragment length(s) may be 166 bps INFO @ Fri, 26 Jun 2020 08:44:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467102/SRX467102.10_model.r INFO @ Fri, 26 Jun 2020 08:44:40: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:44:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:44:44: 11000000 INFO @ Fri, 26 Jun 2020 08:44:50: 12000000 INFO @ Fri, 26 Jun 2020 08:44:50: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:44:56: 13000000 INFO @ Fri, 26 Jun 2020 08:45:01: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:45:01: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:45:01: #1 total tags in treatment: 13814180 INFO @ Fri, 26 Jun 2020 08:45:01: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:45:01: #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 08:45:02: #1 tags after filtering in treatment: 13814180 INFO @ Fri, 26 Jun 2020 08:45:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:45:02: #1 finished! INFO @ Fri, 26 Jun 2020 08:45:02: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:45:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:45:03: #2 number of paired peaks: 360 WARNING @ Fri, 26 Jun 2020 08:45:03: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Fri, 26 Jun 2020 08:45:03: start model_add_line... INFO @ Fri, 26 Jun 2020 08:45:03: start X-correlation... INFO @ Fri, 26 Jun 2020 08:45:03: end of X-cor INFO @ Fri, 26 Jun 2020 08:45:03: #2 finished! INFO @ Fri, 26 Jun 2020 08:45:03: #2 predicted fragment length is 166 bps INFO @ Fri, 26 Jun 2020 08:45:03: #2 alternative fragment length(s) may be 166 bps INFO @ Fri, 26 Jun 2020 08:45:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467102/SRX467102.20_model.r INFO @ Fri, 26 Jun 2020 08:45:03: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:45:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:45:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467102/SRX467102.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:45:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467102/SRX467102.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:45:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467102/SRX467102.05_summits.bed INFO @ Fri, 26 Jun 2020 08:45:08: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6140 records, 4 fields): 9 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:45:13: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:45:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467102/SRX467102.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:45:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467102/SRX467102.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:45:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467102/SRX467102.10_summits.bed INFO @ Fri, 26 Jun 2020 08:45:29: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4227 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:45:36: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:45:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467102/SRX467102.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:45:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467102/SRX467102.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:45:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467102/SRX467102.20_summits.bed INFO @ Fri, 26 Jun 2020 08:45:52: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2356 records, 4 fields): 12 millis CompletedMACS2peakCalling