Job ID = 6456105 SRX = SRX318781 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:54:17 prefetch.2.10.7: 1) Downloading 'SRR927097'... 2020-06-21T10:54:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:57:15 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:57:15 prefetch.2.10.7: 1) 'SRR927097' was downloaded successfully Read 16523290 spots for SRR927097/SRR927097.sra Written 16523290 spots for SRR927097/SRR927097.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:46 16523290 reads; of these: 16523290 (100.00%) were unpaired; of these: 1969956 (11.92%) aligned 0 times 11778854 (71.29%) aligned exactly 1 time 2774480 (16.79%) aligned >1 times 88.08% overall alignment rate Time searching: 00:03:47 Overall time: 00:03:47 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 8 files... [bam_rmdupse_core] 2922490 / 14553334 = 0.2008 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 20:05:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318781/SRX318781.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318781/SRX318781.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318781/SRX318781.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318781/SRX318781.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 20:05:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:05:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:05:44: 1000000 INFO @ Sun, 21 Jun 2020 20:05:49: 2000000 INFO @ Sun, 21 Jun 2020 20:05:54: 3000000 INFO @ Sun, 21 Jun 2020 20:05:58: 4000000 INFO @ Sun, 21 Jun 2020 20:06:03: 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 20:06:07: 6000000 INFO @ Sun, 21 Jun 2020 20:06:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318781/SRX318781.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318781/SRX318781.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318781/SRX318781.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318781/SRX318781.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 20:06:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:06:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:06:12: 7000000 INFO @ Sun, 21 Jun 2020 20:06:13: 1000000 INFO @ Sun, 21 Jun 2020 20:06:17: 8000000 INFO @ Sun, 21 Jun 2020 20:06:17: 2000000 INFO @ Sun, 21 Jun 2020 20:06:21: 9000000 INFO @ Sun, 21 Jun 2020 20:06:22: 3000000 INFO @ Sun, 21 Jun 2020 20:06:27: 10000000 INFO @ Sun, 21 Jun 2020 20:06:27: 4000000 INFO @ Sun, 21 Jun 2020 20:06:31: 11000000 INFO @ Sun, 21 Jun 2020 20:06:31: 5000000 INFO @ Sun, 21 Jun 2020 20:06:35: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:06:35: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:06:35: #1 total tags in treatment: 11630844 INFO @ Sun, 21 Jun 2020 20:06:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:06:35: #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 20:06:35: #1 tags after filtering in treatment: 11630837 INFO @ Sun, 21 Jun 2020 20:06:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:06:35: #1 finished! INFO @ Sun, 21 Jun 2020 20:06:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:06:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:06:36: #2 number of paired peaks: 774 WARNING @ Sun, 21 Jun 2020 20:06:36: Fewer paired peaks (774) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 774 pairs to build model! INFO @ Sun, 21 Jun 2020 20:06:36: start model_add_line... INFO @ Sun, 21 Jun 2020 20:06:36: start X-correlation... INFO @ Sun, 21 Jun 2020 20:06:36: end of X-cor INFO @ Sun, 21 Jun 2020 20:06:36: #2 finished! INFO @ Sun, 21 Jun 2020 20:06:36: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 20:06:36: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 21 Jun 2020 20:06:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318781/SRX318781.05_model.r INFO @ Sun, 21 Jun 2020 20:06:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:06:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:06:36: 6000000 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 20:06:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318781/SRX318781.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318781/SRX318781.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318781/SRX318781.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318781/SRX318781.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 20:06:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:06:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:06:41: 7000000 INFO @ Sun, 21 Jun 2020 20:06:43: 1000000 INFO @ Sun, 21 Jun 2020 20:06:46: 8000000 INFO @ Sun, 21 Jun 2020 20:06:48: 2000000 INFO @ Sun, 21 Jun 2020 20:06:50: 9000000 INFO @ Sun, 21 Jun 2020 20:06:53: 3000000 INFO @ Sun, 21 Jun 2020 20:06:56: 10000000 INFO @ Sun, 21 Jun 2020 20:06:58: 4000000 INFO @ Sun, 21 Jun 2020 20:07:00: 11000000 INFO @ Sun, 21 Jun 2020 20:07:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:07:02: 5000000 INFO @ Sun, 21 Jun 2020 20:07:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:07:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:07:04: #1 total tags in treatment: 11630844 INFO @ Sun, 21 Jun 2020 20:07:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:07:04: #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 20:07:04: #1 tags after filtering in treatment: 11630837 INFO @ Sun, 21 Jun 2020 20:07:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:07:04: #1 finished! INFO @ Sun, 21 Jun 2020 20:07:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:07:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:07:05: #2 number of paired peaks: 774 WARNING @ Sun, 21 Jun 2020 20:07:05: Fewer paired peaks (774) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 774 pairs to build model! INFO @ Sun, 21 Jun 2020 20:07:05: start model_add_line... INFO @ Sun, 21 Jun 2020 20:07:05: start X-correlation... INFO @ Sun, 21 Jun 2020 20:07:05: end of X-cor INFO @ Sun, 21 Jun 2020 20:07:05: #2 finished! INFO @ Sun, 21 Jun 2020 20:07:05: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 20:07:05: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 21 Jun 2020 20:07:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318781/SRX318781.10_model.r INFO @ Sun, 21 Jun 2020 20:07:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:07:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:07:07: 6000000 INFO @ Sun, 21 Jun 2020 20:07:12: 7000000 INFO @ Sun, 21 Jun 2020 20:07:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318781/SRX318781.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:07:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318781/SRX318781.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:07:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318781/SRX318781.05_summits.bed INFO @ Sun, 21 Jun 2020 20:07:14: Done! pass1 - making usageList (456 chroms): 1 millis pass2 - checking and writing primary data (5523 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:07:17: 8000000 INFO @ Sun, 21 Jun 2020 20:07:22: 9000000 INFO @ Sun, 21 Jun 2020 20:07:27: 10000000 INFO @ Sun, 21 Jun 2020 20:07:31: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:07:32: 11000000 INFO @ Sun, 21 Jun 2020 20:07:35: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:07:35: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:07:35: #1 total tags in treatment: 11630844 INFO @ Sun, 21 Jun 2020 20:07:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:07:35: #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 20:07:36: #1 tags after filtering in treatment: 11630837 INFO @ Sun, 21 Jun 2020 20:07:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:07:36: #1 finished! INFO @ Sun, 21 Jun 2020 20:07:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:07:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:07:37: #2 number of paired peaks: 774 WARNING @ Sun, 21 Jun 2020 20:07:37: Fewer paired peaks (774) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 774 pairs to build model! INFO @ Sun, 21 Jun 2020 20:07:37: start model_add_line... INFO @ Sun, 21 Jun 2020 20:07:37: start X-correlation... INFO @ Sun, 21 Jun 2020 20:07:37: end of X-cor INFO @ Sun, 21 Jun 2020 20:07:37: #2 finished! INFO @ Sun, 21 Jun 2020 20:07:37: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 20:07:37: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 21 Jun 2020 20:07:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318781/SRX318781.20_model.r INFO @ Sun, 21 Jun 2020 20:07:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:07:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:07:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318781/SRX318781.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:07:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318781/SRX318781.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:07:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318781/SRX318781.10_summits.bed INFO @ Sun, 21 Jun 2020 20:07:44: Done! pass1 - making usageList (342 chroms): 1 millis pass2 - checking and writing primary data (3181 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:08:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:08:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318781/SRX318781.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:08:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318781/SRX318781.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:08:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318781/SRX318781.20_summits.bed INFO @ Sun, 21 Jun 2020 20:08:14: Done! pass1 - making usageList (153 chroms): 1 millis pass2 - checking and writing primary data (1372 records, 4 fields): 6 millis CompletedMACS2peakCalling