Job ID = 14167554 SRX = SRX4712937 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: 00:06:31 26232448 reads; of these: 26232448 (100.00%) were unpaired; of these: 982330 (3.74%) aligned 0 times 20300148 (77.39%) aligned exactly 1 time 4949970 (18.87%) aligned >1 times 96.26% overall alignment rate Time searching: 00:06:31 Overall time: 00:06:31 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] 6422424 / 25250118 = 0.2544 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 @ Fri, 10 Dec 2021 12:47:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4712937/SRX4712937.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4712937/SRX4712937.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4712937/SRX4712937.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4712937/SRX4712937.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, 10 Dec 2021 12:47:11: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:47:11: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:47:16: 1000000 INFO @ Fri, 10 Dec 2021 12:47:21: 2000000 INFO @ Fri, 10 Dec 2021 12:47:26: 3000000 INFO @ Fri, 10 Dec 2021 12:47:31: 4000000 INFO @ Fri, 10 Dec 2021 12:47:36: 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 @ Fri, 10 Dec 2021 12:47:41: 6000000 INFO @ Fri, 10 Dec 2021 12:47:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4712937/SRX4712937.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4712937/SRX4712937.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4712937/SRX4712937.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4712937/SRX4712937.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, 10 Dec 2021 12:47:41: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:47:41: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:47:46: 7000000 INFO @ Fri, 10 Dec 2021 12:47:47: 1000000 INFO @ Fri, 10 Dec 2021 12:47:51: 8000000 INFO @ Fri, 10 Dec 2021 12:47:53: 2000000 INFO @ Fri, 10 Dec 2021 12:47:56: 9000000 INFO @ Fri, 10 Dec 2021 12:47:59: 3000000 INFO @ Fri, 10 Dec 2021 12:48:01: 10000000 INFO @ Fri, 10 Dec 2021 12:48:05: 4000000 INFO @ Fri, 10 Dec 2021 12:48:06: 11000000 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 @ Fri, 10 Dec 2021 12:48:10: 5000000 INFO @ Fri, 10 Dec 2021 12:48:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4712937/SRX4712937.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4712937/SRX4712937.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4712937/SRX4712937.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4712937/SRX4712937.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, 10 Dec 2021 12:48:11: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:48:11: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:48:12: 12000000 INFO @ Fri, 10 Dec 2021 12:48:16: 6000000 INFO @ Fri, 10 Dec 2021 12:48:16: 1000000 INFO @ Fri, 10 Dec 2021 12:48:17: 13000000 INFO @ Fri, 10 Dec 2021 12:48:22: 2000000 INFO @ Fri, 10 Dec 2021 12:48:22: 7000000 INFO @ Fri, 10 Dec 2021 12:48:22: 14000000 INFO @ Fri, 10 Dec 2021 12:48:27: 15000000 INFO @ Fri, 10 Dec 2021 12:48:27: 3000000 INFO @ Fri, 10 Dec 2021 12:48:27: 8000000 INFO @ Fri, 10 Dec 2021 12:48:32: 4000000 INFO @ Fri, 10 Dec 2021 12:48:33: 16000000 INFO @ Fri, 10 Dec 2021 12:48:33: 9000000 INFO @ Fri, 10 Dec 2021 12:48:37: 5000000 INFO @ Fri, 10 Dec 2021 12:48:38: 17000000 INFO @ Fri, 10 Dec 2021 12:48:39: 10000000 INFO @ Fri, 10 Dec 2021 12:48:43: 6000000 INFO @ Fri, 10 Dec 2021 12:48:43: 18000000 INFO @ Fri, 10 Dec 2021 12:48:44: 11000000 INFO @ Fri, 10 Dec 2021 12:48:48: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 12:48:48: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 12:48:48: #1 total tags in treatment: 18827694 INFO @ Fri, 10 Dec 2021 12:48:48: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:48:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:48:48: 7000000 INFO @ Fri, 10 Dec 2021 12:48:48: #1 tags after filtering in treatment: 18827691 INFO @ Fri, 10 Dec 2021 12:48:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:48:48: #1 finished! INFO @ Fri, 10 Dec 2021 12:48:48: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:48:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:48:50: #2 number of paired peaks: 348 WARNING @ Fri, 10 Dec 2021 12:48:50: Fewer paired peaks (348) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 348 pairs to build model! INFO @ Fri, 10 Dec 2021 12:48:50: start model_add_line... INFO @ Fri, 10 Dec 2021 12:48:50: start X-correlation... INFO @ Fri, 10 Dec 2021 12:48:50: end of X-cor INFO @ Fri, 10 Dec 2021 12:48:50: #2 finished! INFO @ Fri, 10 Dec 2021 12:48:50: #2 predicted fragment length is 137 bps INFO @ Fri, 10 Dec 2021 12:48:50: #2 alternative fragment length(s) may be 137 bps INFO @ Fri, 10 Dec 2021 12:48:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4712937/SRX4712937.05_model.r INFO @ Fri, 10 Dec 2021 12:48:50: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:48:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:48:50: 12000000 INFO @ Fri, 10 Dec 2021 12:48:53: 8000000 INFO @ Fri, 10 Dec 2021 12:48:56: 13000000 INFO @ Fri, 10 Dec 2021 12:48:58: 9000000 INFO @ Fri, 10 Dec 2021 12:49:01: 14000000 INFO @ Fri, 10 Dec 2021 12:49:03: 10000000 INFO @ Fri, 10 Dec 2021 12:49:07: 15000000 INFO @ Fri, 10 Dec 2021 12:49:08: 11000000 INFO @ Fri, 10 Dec 2021 12:49:13: 16000000 INFO @ Fri, 10 Dec 2021 12:49:14: 12000000 INFO @ Fri, 10 Dec 2021 12:49:19: 13000000 INFO @ Fri, 10 Dec 2021 12:49:19: 17000000 INFO @ Fri, 10 Dec 2021 12:49:24: 14000000 INFO @ Fri, 10 Dec 2021 12:49:25: 18000000 INFO @ Fri, 10 Dec 2021 12:49:29: 15000000 INFO @ Fri, 10 Dec 2021 12:49:30: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 12:49:30: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 12:49:30: #1 total tags in treatment: 18827694 INFO @ Fri, 10 Dec 2021 12:49:30: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:49:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:49:30: #1 tags after filtering in treatment: 18827691 INFO @ Fri, 10 Dec 2021 12:49:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:49:30: #1 finished! INFO @ Fri, 10 Dec 2021 12:49:30: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:49:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:49:31: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:49:32: #2 number of paired peaks: 348 WARNING @ Fri, 10 Dec 2021 12:49:32: Fewer paired peaks (348) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 348 pairs to build model! INFO @ Fri, 10 Dec 2021 12:49:32: start model_add_line... INFO @ Fri, 10 Dec 2021 12:49:32: start X-correlation... INFO @ Fri, 10 Dec 2021 12:49:32: end of X-cor INFO @ Fri, 10 Dec 2021 12:49:32: #2 finished! INFO @ Fri, 10 Dec 2021 12:49:32: #2 predicted fragment length is 137 bps INFO @ Fri, 10 Dec 2021 12:49:32: #2 alternative fragment length(s) may be 137 bps INFO @ Fri, 10 Dec 2021 12:49:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4712937/SRX4712937.10_model.r INFO @ Fri, 10 Dec 2021 12:49:32: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:49:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:49:34: 16000000 INFO @ Fri, 10 Dec 2021 12:49:39: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 12:49:44: 18000000 INFO @ Fri, 10 Dec 2021 12:49:49: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 12:49:49: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 12:49:49: #1 total tags in treatment: 18827694 INFO @ Fri, 10 Dec 2021 12:49:49: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:49:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:49:49: #1 tags after filtering in treatment: 18827691 INFO @ Fri, 10 Dec 2021 12:49:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:49:49: #1 finished! INFO @ Fri, 10 Dec 2021 12:49:49: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:49:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:49:51: #2 number of paired peaks: 348 WARNING @ Fri, 10 Dec 2021 12:49:51: Fewer paired peaks (348) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 348 pairs to build model! INFO @ Fri, 10 Dec 2021 12:49:51: start model_add_line... INFO @ Fri, 10 Dec 2021 12:49:51: start X-correlation... INFO @ Fri, 10 Dec 2021 12:49:51: end of X-cor INFO @ Fri, 10 Dec 2021 12:49:51: #2 finished! INFO @ Fri, 10 Dec 2021 12:49:51: #2 predicted fragment length is 137 bps INFO @ Fri, 10 Dec 2021 12:49:51: #2 alternative fragment length(s) may be 137 bps INFO @ Fri, 10 Dec 2021 12:49:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4712937/SRX4712937.20_model.r INFO @ Fri, 10 Dec 2021 12:49:51: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:49:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:49:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4712937/SRX4712937.05_peaks.xls INFO @ Fri, 10 Dec 2021 12:49:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4712937/SRX4712937.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:49:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4712937/SRX4712937.05_summits.bed INFO @ Fri, 10 Dec 2021 12:49:52: Done! pass1 - making usageList (617 chroms): 3 millis pass2 - checking and writing primary data (6138 records, 4 fields): 217 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:50:10: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 12:50:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4712937/SRX4712937.10_peaks.xls INFO @ Fri, 10 Dec 2021 12:50:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4712937/SRX4712937.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:50:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4712937/SRX4712937.10_summits.bed INFO @ Fri, 10 Dec 2021 12:50:29: Done! INFO @ Fri, 10 Dec 2021 12:50:31: #3 Call peaks for each chromosome... pass1 - making usageList (508 chroms): 2 millis pass2 - checking and writing primary data (3845 records, 4 fields): 69 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:50:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4712937/SRX4712937.20_peaks.xls INFO @ Fri, 10 Dec 2021 12:50:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4712937/SRX4712937.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:50:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4712937/SRX4712937.20_summits.bed INFO @ Fri, 10 Dec 2021 12:50:51: Done! pass1 - making usageList (291 chroms): 1 millis pass2 - checking and writing primary data (1880 records, 4 fields): 12 millis CompletedMACS2peakCalling