Job ID = 6498030 SRX = SRX287903 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:15:56 prefetch.2.10.7: 1) Downloading 'SRR870092'... 2020-06-25T23:15:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:18:46 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:18:46 prefetch.2.10.7: 1) 'SRR870092' was downloaded successfully Read 17337186 spots for SRR870092/SRR870092.sra Written 17337186 spots for SRR870092/SRR870092.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: 00:06:44 17337186 reads; of these: 17337186 (100.00%) were unpaired; of these: 858198 (4.95%) aligned 0 times 12373050 (71.37%) aligned exactly 1 time 4105938 (23.68%) aligned >1 times 95.05% overall alignment rate Time searching: 00:06:44 Overall time: 00:06:44 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] 1338221 / 16478988 = 0.0812 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 08:31:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287903/SRX287903.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287903/SRX287903.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287903/SRX287903.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287903/SRX287903.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 08:31:26: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:31:26: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:31:33: 1000000 INFO @ Fri, 26 Jun 2020 08:31:39: 2000000 INFO @ Fri, 26 Jun 2020 08:31:45: 3000000 INFO @ Fri, 26 Jun 2020 08:31:52: 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 08:31:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287903/SRX287903.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287903/SRX287903.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287903/SRX287903.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287903/SRX287903.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 08:31:56: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:31:56: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:31:58: 5000000 INFO @ Fri, 26 Jun 2020 08:32:02: 1000000 INFO @ Fri, 26 Jun 2020 08:32:04: 6000000 INFO @ Fri, 26 Jun 2020 08:32:07: 2000000 INFO @ Fri, 26 Jun 2020 08:32:10: 7000000 INFO @ Fri, 26 Jun 2020 08:32:13: 3000000 INFO @ Fri, 26 Jun 2020 08:32:16: 8000000 INFO @ Fri, 26 Jun 2020 08:32:18: 4000000 INFO @ Fri, 26 Jun 2020 08:32:23: 9000000 INFO @ Fri, 26 Jun 2020 08:32:24: 5000000 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 08:32:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287903/SRX287903.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287903/SRX287903.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287903/SRX287903.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287903/SRX287903.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 08:32:27: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:32:27: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:32:29: 10000000 INFO @ Fri, 26 Jun 2020 08:32:30: 6000000 INFO @ Fri, 26 Jun 2020 08:32:33: 1000000 INFO @ Fri, 26 Jun 2020 08:32:35: 11000000 INFO @ Fri, 26 Jun 2020 08:32:35: 7000000 INFO @ Fri, 26 Jun 2020 08:32:38: 2000000 INFO @ Fri, 26 Jun 2020 08:32:41: 8000000 INFO @ Fri, 26 Jun 2020 08:32:41: 12000000 INFO @ Fri, 26 Jun 2020 08:32:44: 3000000 INFO @ Fri, 26 Jun 2020 08:32:47: 9000000 INFO @ Fri, 26 Jun 2020 08:32:47: 13000000 INFO @ Fri, 26 Jun 2020 08:32:50: 4000000 INFO @ Fri, 26 Jun 2020 08:32:53: 10000000 INFO @ Fri, 26 Jun 2020 08:32:54: 14000000 INFO @ Fri, 26 Jun 2020 08:32:56: 5000000 INFO @ Fri, 26 Jun 2020 08:32:59: 11000000 INFO @ Fri, 26 Jun 2020 08:33:00: 15000000 INFO @ Fri, 26 Jun 2020 08:33:01: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:33:01: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:33:01: #1 total tags in treatment: 15140767 INFO @ Fri, 26 Jun 2020 08:33:01: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:33:01: #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 08:33:01: #1 tags after filtering in treatment: 15140767 INFO @ Fri, 26 Jun 2020 08:33:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:33:01: #1 finished! INFO @ Fri, 26 Jun 2020 08:33:01: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:33:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:33:02: 6000000 INFO @ Fri, 26 Jun 2020 08:33:02: #2 number of paired peaks: 146 WARNING @ Fri, 26 Jun 2020 08:33:02: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Fri, 26 Jun 2020 08:33:02: start model_add_line... INFO @ Fri, 26 Jun 2020 08:33:02: start X-correlation... INFO @ Fri, 26 Jun 2020 08:33:02: end of X-cor INFO @ Fri, 26 Jun 2020 08:33:02: #2 finished! INFO @ Fri, 26 Jun 2020 08:33:02: #2 predicted fragment length is 135 bps INFO @ Fri, 26 Jun 2020 08:33:02: #2 alternative fragment length(s) may be 135 bps INFO @ Fri, 26 Jun 2020 08:33:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287903/SRX287903.05_model.r INFO @ Fri, 26 Jun 2020 08:33:02: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:33:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:33:04: 12000000 INFO @ Fri, 26 Jun 2020 08:33:08: 7000000 INFO @ Fri, 26 Jun 2020 08:33:10: 13000000 INFO @ Fri, 26 Jun 2020 08:33:13: 8000000 INFO @ Fri, 26 Jun 2020 08:33:15: 14000000 INFO @ Fri, 26 Jun 2020 08:33:19: 9000000 INFO @ Fri, 26 Jun 2020 08:33:21: 15000000 INFO @ Fri, 26 Jun 2020 08:33:22: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:33:22: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:33:22: #1 total tags in treatment: 15140767 INFO @ Fri, 26 Jun 2020 08:33:22: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:33:22: #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 08:33:22: #1 tags after filtering in treatment: 15140767 INFO @ Fri, 26 Jun 2020 08:33:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:33:22: #1 finished! INFO @ Fri, 26 Jun 2020 08:33:22: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:33:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:33:23: #2 number of paired peaks: 146 WARNING @ Fri, 26 Jun 2020 08:33:23: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Fri, 26 Jun 2020 08:33:23: start model_add_line... INFO @ Fri, 26 Jun 2020 08:33:23: start X-correlation... INFO @ Fri, 26 Jun 2020 08:33:23: end of X-cor INFO @ Fri, 26 Jun 2020 08:33:23: #2 finished! INFO @ Fri, 26 Jun 2020 08:33:23: #2 predicted fragment length is 135 bps INFO @ Fri, 26 Jun 2020 08:33:23: #2 alternative fragment length(s) may be 135 bps INFO @ Fri, 26 Jun 2020 08:33:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287903/SRX287903.10_model.r INFO @ Fri, 26 Jun 2020 08:33:23: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:33:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:33:24: 10000000 INFO @ Fri, 26 Jun 2020 08:33:29: 11000000 INFO @ Fri, 26 Jun 2020 08:33:35: 12000000 INFO @ Fri, 26 Jun 2020 08:33:38: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:33:40: 13000000 INFO @ Fri, 26 Jun 2020 08:33:45: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:33:51: 15000000 INFO @ Fri, 26 Jun 2020 08:33:52: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:33:52: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:33:52: #1 total tags in treatment: 15140767 INFO @ Fri, 26 Jun 2020 08:33:52: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:33:52: #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 08:33:52: #1 tags after filtering in treatment: 15140767 INFO @ Fri, 26 Jun 2020 08:33:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:33:52: #1 finished! INFO @ Fri, 26 Jun 2020 08:33:52: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:33:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:33:53: #2 number of paired peaks: 146 WARNING @ Fri, 26 Jun 2020 08:33:53: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Fri, 26 Jun 2020 08:33:53: start model_add_line... INFO @ Fri, 26 Jun 2020 08:33:53: start X-correlation... INFO @ Fri, 26 Jun 2020 08:33:53: end of X-cor INFO @ Fri, 26 Jun 2020 08:33:53: #2 finished! INFO @ Fri, 26 Jun 2020 08:33:53: #2 predicted fragment length is 135 bps INFO @ Fri, 26 Jun 2020 08:33:53: #2 alternative fragment length(s) may be 135 bps INFO @ Fri, 26 Jun 2020 08:33:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287903/SRX287903.20_model.r INFO @ Fri, 26 Jun 2020 08:33:53: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:33:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:33:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287903/SRX287903.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:33:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287903/SRX287903.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:33:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287903/SRX287903.05_summits.bed INFO @ Fri, 26 Jun 2020 08:33:56: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4334 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:33:58: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:34:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287903/SRX287903.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:34:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287903/SRX287903.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:34:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287903/SRX287903.10_summits.bed INFO @ Fri, 26 Jun 2020 08:34:15: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2913 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:34:27: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:34:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287903/SRX287903.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:34:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287903/SRX287903.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:34:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287903/SRX287903.20_summits.bed INFO @ Fri, 26 Jun 2020 08:34:44: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1747 records, 4 fields): 4 millis CompletedMACS2peakCalling