Job ID = 16437294 SRX = SRX11638460 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: 00:06:06 24432113 reads; of these: 24432113 (100.00%) were unpaired; of these: 1839579 (7.53%) aligned 0 times 20125344 (82.37%) aligned exactly 1 time 2467190 (10.10%) aligned >1 times 92.47% overall alignment rate Time searching: 00:06:06 Overall time: 00:06:06 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] 3349424 / 22592534 = 0.1483 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 12:30:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX11638460/SRX11638460.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX11638460/SRX11638460.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX11638460/SRX11638460.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX11638460/SRX11638460.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 @ Tue, 02 Aug 2022 12:30:45: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:30:45: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:30:50: 1000000 INFO @ Tue, 02 Aug 2022 12:30:55: 2000000 INFO @ Tue, 02 Aug 2022 12:31:00: 3000000 INFO @ Tue, 02 Aug 2022 12:31:05: 4000000 INFO @ Tue, 02 Aug 2022 12:31:10: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 12:31:15: 6000000 INFO @ Tue, 02 Aug 2022 12:31:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX11638460/SRX11638460.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX11638460/SRX11638460.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX11638460/SRX11638460.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX11638460/SRX11638460.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 @ Tue, 02 Aug 2022 12:31:15: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:31:15: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:31:20: 7000000 INFO @ Tue, 02 Aug 2022 12:31:21: 1000000 INFO @ Tue, 02 Aug 2022 12:31:25: 8000000 INFO @ Tue, 02 Aug 2022 12:31:26: 2000000 INFO @ Tue, 02 Aug 2022 12:31:31: 9000000 INFO @ Tue, 02 Aug 2022 12:31:31: 3000000 INFO @ Tue, 02 Aug 2022 12:31:36: 10000000 INFO @ Tue, 02 Aug 2022 12:31:36: 4000000 INFO @ Tue, 02 Aug 2022 12:31:41: 11000000 INFO @ Tue, 02 Aug 2022 12:31:41: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 12:31:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX11638460/SRX11638460.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX11638460/SRX11638460.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX11638460/SRX11638460.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX11638460/SRX11638460.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 @ Tue, 02 Aug 2022 12:31:45: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:31:45: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:31:46: 12000000 INFO @ Tue, 02 Aug 2022 12:31:47: 6000000 INFO @ Tue, 02 Aug 2022 12:31:51: 1000000 INFO @ Tue, 02 Aug 2022 12:31:52: 13000000 INFO @ Tue, 02 Aug 2022 12:31:52: 7000000 INFO @ Tue, 02 Aug 2022 12:31:56: 2000000 INFO @ Tue, 02 Aug 2022 12:31:57: 14000000 INFO @ Tue, 02 Aug 2022 12:31:58: 8000000 INFO @ Tue, 02 Aug 2022 12:32:02: 3000000 INFO @ Tue, 02 Aug 2022 12:32:02: 15000000 INFO @ Tue, 02 Aug 2022 12:32:03: 9000000 INFO @ Tue, 02 Aug 2022 12:32:07: 4000000 INFO @ Tue, 02 Aug 2022 12:32:08: 16000000 INFO @ Tue, 02 Aug 2022 12:32:08: 10000000 INFO @ Tue, 02 Aug 2022 12:32:13: 5000000 INFO @ Tue, 02 Aug 2022 12:32:14: 17000000 INFO @ Tue, 02 Aug 2022 12:32:14: 11000000 INFO @ Tue, 02 Aug 2022 12:32:18: 6000000 INFO @ Tue, 02 Aug 2022 12:32:19: 18000000 INFO @ Tue, 02 Aug 2022 12:32:19: 12000000 INFO @ Tue, 02 Aug 2022 12:32:23: 7000000 INFO @ Tue, 02 Aug 2022 12:32:25: 13000000 INFO @ Tue, 02 Aug 2022 12:32:25: 19000000 INFO @ Tue, 02 Aug 2022 12:32:27: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 12:32:27: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 12:32:27: #1 total tags in treatment: 19243110 INFO @ Tue, 02 Aug 2022 12:32:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:32:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 12:32:27: #1 tags after filtering in treatment: 19243087 INFO @ Tue, 02 Aug 2022 12:32:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:32:27: #1 finished! INFO @ Tue, 02 Aug 2022 12:32:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:32:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:32:29: 8000000 INFO @ Tue, 02 Aug 2022 12:32:29: #2 number of paired peaks: 624 WARNING @ Tue, 02 Aug 2022 12:32:29: Fewer paired peaks (624) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 624 pairs to build model! INFO @ Tue, 02 Aug 2022 12:32:29: start model_add_line... INFO @ Tue, 02 Aug 2022 12:32:29: start X-correlation... INFO @ Tue, 02 Aug 2022 12:32:29: end of X-cor INFO @ Tue, 02 Aug 2022 12:32:29: #2 finished! INFO @ Tue, 02 Aug 2022 12:32:29: #2 predicted fragment length is 144 bps INFO @ Tue, 02 Aug 2022 12:32:29: #2 alternative fragment length(s) may be 144 bps INFO @ Tue, 02 Aug 2022 12:32:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX11638460/SRX11638460.05_model.r INFO @ Tue, 02 Aug 2022 12:32:29: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:32:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:32:30: 14000000 INFO @ Tue, 02 Aug 2022 12:32:34: 9000000 INFO @ Tue, 02 Aug 2022 12:32:35: 15000000 INFO @ Tue, 02 Aug 2022 12:32:39: 10000000 INFO @ Tue, 02 Aug 2022 12:32:41: 16000000 INFO @ Tue, 02 Aug 2022 12:32:44: 11000000 INFO @ Tue, 02 Aug 2022 12:32:46: 17000000 INFO @ Tue, 02 Aug 2022 12:32:49: 12000000 INFO @ Tue, 02 Aug 2022 12:32:51: 18000000 INFO @ Tue, 02 Aug 2022 12:32:54: 13000000 INFO @ Tue, 02 Aug 2022 12:32:56: 19000000 INFO @ Tue, 02 Aug 2022 12:32:58: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 12:32:58: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 12:32:58: #1 total tags in treatment: 19243110 INFO @ Tue, 02 Aug 2022 12:32:58: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:32:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 12:32:59: #1 tags after filtering in treatment: 19243087 INFO @ Tue, 02 Aug 2022 12:32:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:32:59: #1 finished! INFO @ Tue, 02 Aug 2022 12:32:59: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:32:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:32:59: 14000000 INFO @ Tue, 02 Aug 2022 12:33:00: #2 number of paired peaks: 624 WARNING @ Tue, 02 Aug 2022 12:33:00: Fewer paired peaks (624) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 624 pairs to build model! INFO @ Tue, 02 Aug 2022 12:33:00: start model_add_line... INFO @ Tue, 02 Aug 2022 12:33:00: start X-correlation... INFO @ Tue, 02 Aug 2022 12:33:00: end of X-cor INFO @ Tue, 02 Aug 2022 12:33:00: #2 finished! INFO @ Tue, 02 Aug 2022 12:33:00: #2 predicted fragment length is 144 bps INFO @ Tue, 02 Aug 2022 12:33:00: #2 alternative fragment length(s) may be 144 bps INFO @ Tue, 02 Aug 2022 12:33:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX11638460/SRX11638460.10_model.r INFO @ Tue, 02 Aug 2022 12:33:00: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:33:00: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 12:33:05: 15000000 INFO @ Tue, 02 Aug 2022 12:33:10: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:33:10: 16000000 INFO @ Tue, 02 Aug 2022 12:33:15: 17000000 INFO @ Tue, 02 Aug 2022 12:33:21: 18000000 INFO @ Tue, 02 Aug 2022 12:33:26: 19000000 INFO @ Tue, 02 Aug 2022 12:33:27: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 12:33:27: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 12:33:27: #1 total tags in treatment: 19243110 INFO @ Tue, 02 Aug 2022 12:33:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:33:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 12:33:28: #1 tags after filtering in treatment: 19243087 INFO @ Tue, 02 Aug 2022 12:33:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:33:28: #1 finished! INFO @ Tue, 02 Aug 2022 12:33:28: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:33:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:33:29: #2 number of paired peaks: 624 WARNING @ Tue, 02 Aug 2022 12:33:29: Fewer paired peaks (624) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 624 pairs to build model! INFO @ Tue, 02 Aug 2022 12:33:29: start model_add_line... INFO @ Tue, 02 Aug 2022 12:33:29: start X-correlation... INFO @ Tue, 02 Aug 2022 12:33:29: end of X-cor INFO @ Tue, 02 Aug 2022 12:33:29: #2 finished! INFO @ Tue, 02 Aug 2022 12:33:29: #2 predicted fragment length is 144 bps INFO @ Tue, 02 Aug 2022 12:33:29: #2 alternative fragment length(s) may be 144 bps INFO @ Tue, 02 Aug 2022 12:33:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX11638460/SRX11638460.20_model.r INFO @ Tue, 02 Aug 2022 12:33:29: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:33:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:33:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX11638460/SRX11638460.05_peaks.xls INFO @ Tue, 02 Aug 2022 12:33:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX11638460/SRX11638460.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:33:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX11638460/SRX11638460.05_summits.bed INFO @ Tue, 02 Aug 2022 12:33:31: Done! pass1 - making usageList (171 chroms): 2 millis pass2 - checking and writing primary data (11093 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:33:41: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 12:34:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX11638460/SRX11638460.10_peaks.xls INFO @ Tue, 02 Aug 2022 12:34:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX11638460/SRX11638460.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:34:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX11638460/SRX11638460.10_summits.bed INFO @ Tue, 02 Aug 2022 12:34:03: Done! pass1 - making usageList (93 chroms): 2 millis pass2 - checking and writing primary data (6699 records, 4 fields): 242 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:34:09: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:34:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX11638460/SRX11638460.20_peaks.xls INFO @ Tue, 02 Aug 2022 12:34:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX11638460/SRX11638460.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:34:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX11638460/SRX11638460.20_summits.bed INFO @ Tue, 02 Aug 2022 12:34:30: Done! pass1 - making usageList (64 chroms): 1 millis pass2 - checking and writing primary data (3086 records, 4 fields): 43 millis CompletedMACS2peakCalling