Job ID = 6529714 SRX = SRX4047179 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: 00:02:19 11679339 reads; of these: 11679339 (100.00%) were unpaired; of these: 801078 (6.86%) aligned 0 times 9095060 (77.87%) aligned exactly 1 time 1783201 (15.27%) aligned >1 times 93.14% overall alignment rate Time searching: 00:02:20 Overall time: 00:02:20 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_rmdupse_core] 1669188 / 10878261 = 0.1534 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 @ Tue, 30 Jun 2020 02:31:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4047179/SRX4047179.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4047179/SRX4047179.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4047179/SRX4047179.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4047179/SRX4047179.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, 30 Jun 2020 02:31:52: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:31:52: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:31:58: 1000000 INFO @ Tue, 30 Jun 2020 02:32:04: 2000000 INFO @ Tue, 30 Jun 2020 02:32:09: 3000000 INFO @ Tue, 30 Jun 2020 02:32:15: 4000000 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 @ Tue, 30 Jun 2020 02:32:21: 5000000 INFO @ Tue, 30 Jun 2020 02:32:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4047179/SRX4047179.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4047179/SRX4047179.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4047179/SRX4047179.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4047179/SRX4047179.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, 30 Jun 2020 02:32:22: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:32:22: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:32:27: 6000000 INFO @ Tue, 30 Jun 2020 02:32:28: 1000000 INFO @ Tue, 30 Jun 2020 02:32:33: 7000000 INFO @ Tue, 30 Jun 2020 02:32:34: 2000000 INFO @ Tue, 30 Jun 2020 02:32:39: 8000000 INFO @ Tue, 30 Jun 2020 02:32:41: 3000000 INFO @ Tue, 30 Jun 2020 02:32:45: 9000000 INFO @ Tue, 30 Jun 2020 02:32:47: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 02:32:47: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 02:32:47: #1 total tags in treatment: 9209073 INFO @ Tue, 30 Jun 2020 02:32:47: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:32:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:32:47: 4000000 INFO @ Tue, 30 Jun 2020 02:32:47: #1 tags after filtering in treatment: 9209038 INFO @ Tue, 30 Jun 2020 02:32:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:32:47: #1 finished! INFO @ Tue, 30 Jun 2020 02:32:47: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:32:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:32:48: #2 number of paired peaks: 343 WARNING @ Tue, 30 Jun 2020 02:32:48: Fewer paired peaks (343) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 343 pairs to build model! INFO @ Tue, 30 Jun 2020 02:32:48: start model_add_line... INFO @ Tue, 30 Jun 2020 02:32:48: start X-correlation... INFO @ Tue, 30 Jun 2020 02:32:48: end of X-cor INFO @ Tue, 30 Jun 2020 02:32:48: #2 finished! INFO @ Tue, 30 Jun 2020 02:32:48: #2 predicted fragment length is 107 bps INFO @ Tue, 30 Jun 2020 02:32:48: #2 alternative fragment length(s) may be 107 bps INFO @ Tue, 30 Jun 2020 02:32:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4047179/SRX4047179.05_model.r INFO @ Tue, 30 Jun 2020 02:32:48: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:32:48: #3 Pre-compute pvalue-qvalue table... 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 @ Tue, 30 Jun 2020 02:32:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4047179/SRX4047179.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4047179/SRX4047179.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4047179/SRX4047179.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4047179/SRX4047179.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, 30 Jun 2020 02:32:52: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:32:52: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:32:53: 5000000 INFO @ Tue, 30 Jun 2020 02:32:59: 1000000 INFO @ Tue, 30 Jun 2020 02:32:59: 6000000 INFO @ Tue, 30 Jun 2020 02:33:05: 2000000 INFO @ Tue, 30 Jun 2020 02:33:05: 7000000 INFO @ Tue, 30 Jun 2020 02:33:11: 3000000 INFO @ Tue, 30 Jun 2020 02:33:12: 8000000 INFO @ Tue, 30 Jun 2020 02:33:12: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:33:18: 4000000 INFO @ Tue, 30 Jun 2020 02:33:18: 9000000 INFO @ Tue, 30 Jun 2020 02:33:19: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 02:33:19: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 02:33:19: #1 total tags in treatment: 9209073 INFO @ Tue, 30 Jun 2020 02:33:19: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:33:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:33:20: #1 tags after filtering in treatment: 9209038 INFO @ Tue, 30 Jun 2020 02:33:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:33:20: #1 finished! INFO @ Tue, 30 Jun 2020 02:33:20: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:33:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:33:21: #2 number of paired peaks: 343 WARNING @ Tue, 30 Jun 2020 02:33:21: Fewer paired peaks (343) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 343 pairs to build model! INFO @ Tue, 30 Jun 2020 02:33:21: start model_add_line... INFO @ Tue, 30 Jun 2020 02:33:21: start X-correlation... INFO @ Tue, 30 Jun 2020 02:33:21: end of X-cor INFO @ Tue, 30 Jun 2020 02:33:21: #2 finished! INFO @ Tue, 30 Jun 2020 02:33:21: #2 predicted fragment length is 107 bps INFO @ Tue, 30 Jun 2020 02:33:21: #2 alternative fragment length(s) may be 107 bps INFO @ Tue, 30 Jun 2020 02:33:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4047179/SRX4047179.10_model.r INFO @ Tue, 30 Jun 2020 02:33:21: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:33:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:33:24: 5000000 INFO @ Tue, 30 Jun 2020 02:33:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4047179/SRX4047179.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:33:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4047179/SRX4047179.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:33:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4047179/SRX4047179.05_summits.bed INFO @ Tue, 30 Jun 2020 02:33:25: Done! pass1 - making usageList (408 chroms): 2 millis pass2 - checking and writing primary data (5269 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:33:30: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:33:36: 7000000 INFO @ Tue, 30 Jun 2020 02:33:42: 8000000 INFO @ Tue, 30 Jun 2020 02:33:44: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:33:48: 9000000 INFO @ Tue, 30 Jun 2020 02:33:50: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 02:33:50: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 02:33:50: #1 total tags in treatment: 9209073 INFO @ Tue, 30 Jun 2020 02:33:50: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:33:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:33:50: #1 tags after filtering in treatment: 9209038 INFO @ Tue, 30 Jun 2020 02:33:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:33:50: #1 finished! INFO @ Tue, 30 Jun 2020 02:33:50: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:33:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:33:51: #2 number of paired peaks: 343 WARNING @ Tue, 30 Jun 2020 02:33:51: Fewer paired peaks (343) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 343 pairs to build model! INFO @ Tue, 30 Jun 2020 02:33:51: start model_add_line... INFO @ Tue, 30 Jun 2020 02:33:51: start X-correlation... INFO @ Tue, 30 Jun 2020 02:33:51: end of X-cor INFO @ Tue, 30 Jun 2020 02:33:51: #2 finished! INFO @ Tue, 30 Jun 2020 02:33:51: #2 predicted fragment length is 107 bps INFO @ Tue, 30 Jun 2020 02:33:51: #2 alternative fragment length(s) may be 107 bps INFO @ Tue, 30 Jun 2020 02:33:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4047179/SRX4047179.20_model.r INFO @ Tue, 30 Jun 2020 02:33:51: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:33:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:33:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4047179/SRX4047179.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:33:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4047179/SRX4047179.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:33:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4047179/SRX4047179.10_summits.bed INFO @ Tue, 30 Jun 2020 02:33:56: Done! pass1 - making usageList (210 chroms): 1 millis pass2 - checking and writing primary data (1323 records, 4 fields): 9 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:34:15: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:34:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4047179/SRX4047179.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:34:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4047179/SRX4047179.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:34:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4047179/SRX4047179.20_summits.bed INFO @ Tue, 30 Jun 2020 02:34:28: Done! pass1 - making usageList (108 chroms): 1 millis pass2 - checking and writing primary data (293 records, 4 fields): 5 millis CompletedMACS2peakCalling