Job ID = 14171791 SRX = SRX9986145 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: 00:06:48 26522444 reads; of these: 26522444 (100.00%) were unpaired; of these: 1691008 (6.38%) aligned 0 times 15271432 (57.58%) aligned exactly 1 time 9560004 (36.04%) aligned >1 times 93.62% overall alignment rate Time searching: 00:06:48 Overall time: 00:06:48 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] 8275691 / 24831436 = 0.3333 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 13:04:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986145/SRX9986145.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986145/SRX9986145.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986145/SRX9986145.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986145/SRX9986145.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 13:04:08: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:04:08: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:04:14: 1000000 INFO @ Sat, 11 Dec 2021 13:04:20: 2000000 INFO @ Sat, 11 Dec 2021 13:04:27: 3000000 INFO @ Sat, 11 Dec 2021 13:04:33: 4000000 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 13:04:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986145/SRX9986145.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986145/SRX9986145.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986145/SRX9986145.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986145/SRX9986145.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 13:04:38: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:04:38: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:04:40: 5000000 INFO @ Sat, 11 Dec 2021 13:04:44: 1000000 INFO @ Sat, 11 Dec 2021 13:04:46: 6000000 INFO @ Sat, 11 Dec 2021 13:04:50: 2000000 INFO @ Sat, 11 Dec 2021 13:04:53: 7000000 INFO @ Sat, 11 Dec 2021 13:04:56: 3000000 INFO @ Sat, 11 Dec 2021 13:05:00: 8000000 INFO @ Sat, 11 Dec 2021 13:05:02: 4000000 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 13:05:07: 9000000 INFO @ Sat, 11 Dec 2021 13:05:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986145/SRX9986145.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986145/SRX9986145.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986145/SRX9986145.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986145/SRX9986145.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 13:05:08: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:05:08: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:05:08: 5000000 INFO @ Sat, 11 Dec 2021 13:05:14: 1000000 INFO @ Sat, 11 Dec 2021 13:05:14: 10000000 INFO @ Sat, 11 Dec 2021 13:05:14: 6000000 INFO @ Sat, 11 Dec 2021 13:05:20: 7000000 INFO @ Sat, 11 Dec 2021 13:05:20: 2000000 INFO @ Sat, 11 Dec 2021 13:05:21: 11000000 INFO @ Sat, 11 Dec 2021 13:05:26: 8000000 INFO @ Sat, 11 Dec 2021 13:05:26: 3000000 INFO @ Sat, 11 Dec 2021 13:05:28: 12000000 INFO @ Sat, 11 Dec 2021 13:05:32: 9000000 INFO @ Sat, 11 Dec 2021 13:05:32: 4000000 INFO @ Sat, 11 Dec 2021 13:05:34: 13000000 INFO @ Sat, 11 Dec 2021 13:05:39: 10000000 INFO @ Sat, 11 Dec 2021 13:05:39: 5000000 INFO @ Sat, 11 Dec 2021 13:05:42: 14000000 INFO @ Sat, 11 Dec 2021 13:05:45: 11000000 INFO @ Sat, 11 Dec 2021 13:05:45: 6000000 INFO @ Sat, 11 Dec 2021 13:05:48: 15000000 INFO @ Sat, 11 Dec 2021 13:05:51: 12000000 INFO @ Sat, 11 Dec 2021 13:05:51: 7000000 INFO @ Sat, 11 Dec 2021 13:05:55: 16000000 INFO @ Sat, 11 Dec 2021 13:05:57: 13000000 INFO @ Sat, 11 Dec 2021 13:05:57: 8000000 INFO @ Sat, 11 Dec 2021 13:05:59: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:05:59: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:05:59: #1 total tags in treatment: 16555745 INFO @ Sat, 11 Dec 2021 13:05:59: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:05:59: #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 13:05:59: #1 tags after filtering in treatment: 16555656 INFO @ Sat, 11 Dec 2021 13:05:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:05:59: #1 finished! INFO @ Sat, 11 Dec 2021 13:05:59: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:05:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:06:01: #2 number of paired peaks: 898 WARNING @ Sat, 11 Dec 2021 13:06:01: Fewer paired peaks (898) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 898 pairs to build model! INFO @ Sat, 11 Dec 2021 13:06:01: start model_add_line... INFO @ Sat, 11 Dec 2021 13:06:01: start X-correlation... INFO @ Sat, 11 Dec 2021 13:06:01: end of X-cor INFO @ Sat, 11 Dec 2021 13:06:01: #2 finished! INFO @ Sat, 11 Dec 2021 13:06:01: #2 predicted fragment length is 188 bps INFO @ Sat, 11 Dec 2021 13:06:01: #2 alternative fragment length(s) may be 188 bps INFO @ Sat, 11 Dec 2021 13:06:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986145/SRX9986145.05_model.r INFO @ Sat, 11 Dec 2021 13:06:01: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:06:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:06:03: 9000000 INFO @ Sat, 11 Dec 2021 13:06:04: 14000000 INFO @ Sat, 11 Dec 2021 13:06:09: 10000000 INFO @ Sat, 11 Dec 2021 13:06:10: 15000000 INFO @ Sat, 11 Dec 2021 13:06:15: 11000000 INFO @ Sat, 11 Dec 2021 13:06:16: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:06:19: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:06:19: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:06:19: #1 total tags in treatment: 16555745 INFO @ Sat, 11 Dec 2021 13:06:19: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:06:19: #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 13:06:20: #1 tags after filtering in treatment: 16555656 INFO @ Sat, 11 Dec 2021 13:06:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:06:20: #1 finished! INFO @ Sat, 11 Dec 2021 13:06:20: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:06:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:06:21: #2 number of paired peaks: 898 WARNING @ Sat, 11 Dec 2021 13:06:21: Fewer paired peaks (898) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 898 pairs to build model! INFO @ Sat, 11 Dec 2021 13:06:21: start model_add_line... INFO @ Sat, 11 Dec 2021 13:06:21: start X-correlation... INFO @ Sat, 11 Dec 2021 13:06:21: end of X-cor INFO @ Sat, 11 Dec 2021 13:06:21: #2 finished! INFO @ Sat, 11 Dec 2021 13:06:21: #2 predicted fragment length is 188 bps INFO @ Sat, 11 Dec 2021 13:06:21: #2 alternative fragment length(s) may be 188 bps INFO @ Sat, 11 Dec 2021 13:06:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986145/SRX9986145.10_model.r INFO @ Sat, 11 Dec 2021 13:06:21: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:06:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:06:21: 12000000 INFO @ Sat, 11 Dec 2021 13:06:27: 13000000 INFO @ Sat, 11 Dec 2021 13:06:32: 14000000 INFO @ Sat, 11 Dec 2021 13:06:36: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:06:38: 15000000 INFO @ Sat, 11 Dec 2021 13:06:43: 16000000 INFO @ Sat, 11 Dec 2021 13:06:46: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:06:46: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:06:46: #1 total tags in treatment: 16555745 INFO @ Sat, 11 Dec 2021 13:06:46: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:06:46: #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 13:06:47: #1 tags after filtering in treatment: 16555656 INFO @ Sat, 11 Dec 2021 13:06:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:06:47: #1 finished! INFO @ Sat, 11 Dec 2021 13:06:47: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:06:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:06:48: #2 number of paired peaks: 898 WARNING @ Sat, 11 Dec 2021 13:06:48: Fewer paired peaks (898) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 898 pairs to build model! INFO @ Sat, 11 Dec 2021 13:06:48: start model_add_line... INFO @ Sat, 11 Dec 2021 13:06:48: start X-correlation... INFO @ Sat, 11 Dec 2021 13:06:48: end of X-cor INFO @ Sat, 11 Dec 2021 13:06:48: #2 finished! INFO @ Sat, 11 Dec 2021 13:06:48: #2 predicted fragment length is 188 bps INFO @ Sat, 11 Dec 2021 13:06:48: #2 alternative fragment length(s) may be 188 bps INFO @ Sat, 11 Dec 2021 13:06:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986145/SRX9986145.20_model.r INFO @ Sat, 11 Dec 2021 13:06:48: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:06:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:06:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986145/SRX9986145.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:06:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986145/SRX9986145.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:06:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986145/SRX9986145.05_summits.bed INFO @ Sat, 11 Dec 2021 13:06:54: Done! pass1 - making usageList (660 chroms): 4 millis pass2 - checking and writing primary data (20496 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:06:57: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:07:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986145/SRX9986145.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:07:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986145/SRX9986145.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:07:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986145/SRX9986145.10_summits.bed INFO @ Sat, 11 Dec 2021 13:07:15: Done! pass1 - making usageList (566 chroms): 2 millis pass2 - checking and writing primary data (6543 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:07:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:07:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986145/SRX9986145.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:07:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986145/SRX9986145.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:07:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986145/SRX9986145.20_summits.bed INFO @ Sat, 11 Dec 2021 13:07:39: Done! pass1 - making usageList (483 chroms): 1 millis pass2 - checking and writing primary data (1493 records, 4 fields): 14 millis CompletedMACS2peakCalling