Job ID = 14172624 SRX = SRX9891434 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:07:20 30320949 reads; of these: 30320949 (100.00%) were unpaired; of these: 5652575 (18.64%) aligned 0 times 21160687 (69.79%) aligned exactly 1 time 3507687 (11.57%) aligned >1 times 81.36% overall alignment rate Time searching: 00:07:20 Overall time: 00:07:20 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 12 files... [bam_rmdupse_core] 3045563 / 24668374 = 0.1235 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 16:28:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9891434/SRX9891434.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9891434/SRX9891434.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9891434/SRX9891434.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9891434/SRX9891434.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 @ Sat, 11 Dec 2021 16:28:11: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:28:11: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:28:17: 1000000 INFO @ Sat, 11 Dec 2021 16:28:22: 2000000 INFO @ Sat, 11 Dec 2021 16:28:28: 3000000 INFO @ Sat, 11 Dec 2021 16:28:33: 4000000 INFO @ Sat, 11 Dec 2021 16:28:39: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 16:28:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9891434/SRX9891434.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9891434/SRX9891434.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9891434/SRX9891434.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9891434/SRX9891434.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 @ Sat, 11 Dec 2021 16:28:41: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:28:41: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:28:45: 6000000 INFO @ Sat, 11 Dec 2021 16:28:49: 1000000 INFO @ Sat, 11 Dec 2021 16:28:51: 7000000 INFO @ Sat, 11 Dec 2021 16:28:56: 2000000 INFO @ Sat, 11 Dec 2021 16:28:58: 8000000 INFO @ Sat, 11 Dec 2021 16:29:04: 3000000 INFO @ Sat, 11 Dec 2021 16:29:04: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 16:29:11: 10000000 INFO @ Sat, 11 Dec 2021 16:29:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9891434/SRX9891434.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9891434/SRX9891434.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9891434/SRX9891434.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9891434/SRX9891434.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 @ Sat, 11 Dec 2021 16:29:11: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:29:11: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:29:11: 4000000 INFO @ Sat, 11 Dec 2021 16:29:18: 11000000 INFO @ Sat, 11 Dec 2021 16:29:18: 1000000 INFO @ Sat, 11 Dec 2021 16:29:19: 5000000 INFO @ Sat, 11 Dec 2021 16:29:24: 12000000 INFO @ Sat, 11 Dec 2021 16:29:24: 2000000 INFO @ Sat, 11 Dec 2021 16:29:27: 6000000 INFO @ Sat, 11 Dec 2021 16:29:31: 13000000 INFO @ Sat, 11 Dec 2021 16:29:31: 3000000 INFO @ Sat, 11 Dec 2021 16:29:34: 7000000 INFO @ Sat, 11 Dec 2021 16:29:37: 14000000 INFO @ Sat, 11 Dec 2021 16:29:38: 4000000 INFO @ Sat, 11 Dec 2021 16:29:41: 8000000 INFO @ Sat, 11 Dec 2021 16:29:44: 15000000 INFO @ Sat, 11 Dec 2021 16:29:44: 5000000 INFO @ Sat, 11 Dec 2021 16:29:48: 9000000 INFO @ Sat, 11 Dec 2021 16:29:51: 16000000 INFO @ Sat, 11 Dec 2021 16:29:51: 6000000 INFO @ Sat, 11 Dec 2021 16:29:56: 10000000 INFO @ Sat, 11 Dec 2021 16:29:57: 17000000 INFO @ Sat, 11 Dec 2021 16:29:57: 7000000 INFO @ Sat, 11 Dec 2021 16:30:03: 11000000 INFO @ Sat, 11 Dec 2021 16:30:04: 8000000 INFO @ Sat, 11 Dec 2021 16:30:04: 18000000 INFO @ Sat, 11 Dec 2021 16:30:11: 9000000 INFO @ Sat, 11 Dec 2021 16:30:11: 12000000 INFO @ Sat, 11 Dec 2021 16:30:11: 19000000 INFO @ Sat, 11 Dec 2021 16:30:17: 10000000 INFO @ Sat, 11 Dec 2021 16:30:17: 20000000 INFO @ Sat, 11 Dec 2021 16:30:18: 13000000 INFO @ Sat, 11 Dec 2021 16:30:24: 11000000 INFO @ Sat, 11 Dec 2021 16:30:24: 21000000 INFO @ Sat, 11 Dec 2021 16:30:25: 14000000 INFO @ Sat, 11 Dec 2021 16:30:29: #1 tag size is determined as 60 bps INFO @ Sat, 11 Dec 2021 16:30:29: #1 tag size = 60 INFO @ Sat, 11 Dec 2021 16:30:29: #1 total tags in treatment: 21622811 INFO @ Sat, 11 Dec 2021 16:30:29: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:30:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 16:30:29: #1 tags after filtering in treatment: 21622798 INFO @ Sat, 11 Dec 2021 16:30:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 16:30:29: #1 finished! INFO @ Sat, 11 Dec 2021 16:30:29: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:30:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:30:30: 12000000 INFO @ Sat, 11 Dec 2021 16:30:31: #2 number of paired peaks: 138 WARNING @ Sat, 11 Dec 2021 16:30:31: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Sat, 11 Dec 2021 16:30:31: start model_add_line... INFO @ Sat, 11 Dec 2021 16:30:31: start X-correlation... INFO @ Sat, 11 Dec 2021 16:30:31: end of X-cor INFO @ Sat, 11 Dec 2021 16:30:31: #2 finished! INFO @ Sat, 11 Dec 2021 16:30:31: #2 predicted fragment length is 128 bps INFO @ Sat, 11 Dec 2021 16:30:31: #2 alternative fragment length(s) may be 128 bps INFO @ Sat, 11 Dec 2021 16:30:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9891434/SRX9891434.05_model.r INFO @ Sat, 11 Dec 2021 16:30:31: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:30:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:30:33: 15000000 INFO @ Sat, 11 Dec 2021 16:30:37: 13000000 INFO @ Sat, 11 Dec 2021 16:30:40: 16000000 INFO @ Sat, 11 Dec 2021 16:30:43: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 16:30:47: 17000000 INFO @ Sat, 11 Dec 2021 16:30:50: 15000000 INFO @ Sat, 11 Dec 2021 16:30:55: 18000000 INFO @ Sat, 11 Dec 2021 16:30:56: 16000000 INFO @ Sat, 11 Dec 2021 16:31:03: 19000000 INFO @ Sat, 11 Dec 2021 16:31:03: 17000000 INFO @ Sat, 11 Dec 2021 16:31:10: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:31:10: 18000000 INFO @ Sat, 11 Dec 2021 16:31:10: 20000000 INFO @ Sat, 11 Dec 2021 16:31:16: 19000000 INFO @ Sat, 11 Dec 2021 16:31:18: 21000000 INFO @ Sat, 11 Dec 2021 16:31:23: #1 tag size is determined as 60 bps INFO @ Sat, 11 Dec 2021 16:31:23: #1 tag size = 60 INFO @ Sat, 11 Dec 2021 16:31:23: #1 total tags in treatment: 21622811 INFO @ Sat, 11 Dec 2021 16:31:23: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:31:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 16:31:23: 20000000 INFO @ Sat, 11 Dec 2021 16:31:23: #1 tags after filtering in treatment: 21622798 INFO @ Sat, 11 Dec 2021 16:31:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 16:31:23: #1 finished! INFO @ Sat, 11 Dec 2021 16:31:23: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:31:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:31:25: #2 number of paired peaks: 138 WARNING @ Sat, 11 Dec 2021 16:31:25: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Sat, 11 Dec 2021 16:31:25: start model_add_line... INFO @ Sat, 11 Dec 2021 16:31:25: start X-correlation... INFO @ Sat, 11 Dec 2021 16:31:25: end of X-cor INFO @ Sat, 11 Dec 2021 16:31:25: #2 finished! INFO @ Sat, 11 Dec 2021 16:31:25: #2 predicted fragment length is 128 bps INFO @ Sat, 11 Dec 2021 16:31:25: #2 alternative fragment length(s) may be 128 bps INFO @ Sat, 11 Dec 2021 16:31:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9891434/SRX9891434.10_model.r INFO @ Sat, 11 Dec 2021 16:31:25: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:31:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:31:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9891434/SRX9891434.05_peaks.xls INFO @ Sat, 11 Dec 2021 16:31:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9891434/SRX9891434.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:31:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9891434/SRX9891434.05_summits.bed INFO @ Sat, 11 Dec 2021 16:31:28: Done! pass1 - making usageList (569 chroms): 1 millis pass2 - checking and writing primary data (3927 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:31:29: 21000000 INFO @ Sat, 11 Dec 2021 16:31:33: #1 tag size is determined as 60 bps INFO @ Sat, 11 Dec 2021 16:31:33: #1 tag size = 60 INFO @ Sat, 11 Dec 2021 16:31:33: #1 total tags in treatment: 21622811 INFO @ Sat, 11 Dec 2021 16:31:33: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:31:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 16:31:34: #1 tags after filtering in treatment: 21622798 INFO @ Sat, 11 Dec 2021 16:31:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 16:31:34: #1 finished! INFO @ Sat, 11 Dec 2021 16:31:34: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:31:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:31:35: #2 number of paired peaks: 138 WARNING @ Sat, 11 Dec 2021 16:31:35: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Sat, 11 Dec 2021 16:31:35: start model_add_line... INFO @ Sat, 11 Dec 2021 16:31:35: start X-correlation... INFO @ Sat, 11 Dec 2021 16:31:35: end of X-cor INFO @ Sat, 11 Dec 2021 16:31:35: #2 finished! INFO @ Sat, 11 Dec 2021 16:31:35: #2 predicted fragment length is 128 bps INFO @ Sat, 11 Dec 2021 16:31:35: #2 alternative fragment length(s) may be 128 bps INFO @ Sat, 11 Dec 2021 16:31:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9891434/SRX9891434.20_model.r INFO @ Sat, 11 Dec 2021 16:31:35: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:31:35: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 16:32:02: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:32:15: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:32:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9891434/SRX9891434.10_peaks.xls INFO @ Sat, 11 Dec 2021 16:32:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9891434/SRX9891434.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:32:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9891434/SRX9891434.10_summits.bed INFO @ Sat, 11 Dec 2021 16:32:20: Done! pass1 - making usageList (442 chroms): 2 millis pass2 - checking and writing primary data (1993 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:32:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9891434/SRX9891434.20_peaks.xls INFO @ Sat, 11 Dec 2021 16:32:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9891434/SRX9891434.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:32:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9891434/SRX9891434.20_summits.bed INFO @ Sat, 11 Dec 2021 16:32:33: Done! pass1 - making usageList (206 chroms): 1 millis pass2 - checking and writing primary data (921 records, 4 fields): 8 millis CompletedMACS2peakCalling