Job ID = 6529193 SRX = SRX033324 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: 00:04:07 21637238 reads; of these: 21637238 (100.00%) were unpaired; of these: 593017 (2.74%) aligned 0 times 17484219 (80.81%) aligned exactly 1 time 3560002 (16.45%) aligned >1 times 97.26% overall alignment rate Time searching: 00:04:07 Overall time: 00:04:07 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 8 files... [bam_rmdupse_core] 3178845 / 21044221 = 0.1511 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 01:59:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX033324/SRX033324.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX033324/SRX033324.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX033324/SRX033324.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX033324/SRX033324.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 01:59:41: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:59:41: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:59:47: 1000000 INFO @ Tue, 30 Jun 2020 01:59:52: 2000000 INFO @ Tue, 30 Jun 2020 01:59:58: 3000000 INFO @ Tue, 30 Jun 2020 02:00:03: 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 02:00:09: 5000000 INFO @ Tue, 30 Jun 2020 02:00:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX033324/SRX033324.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX033324/SRX033324.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX033324/SRX033324.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX033324/SRX033324.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 02:00:11: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:00:11: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:00:14: 6000000 INFO @ Tue, 30 Jun 2020 02:00:18: 1000000 INFO @ Tue, 30 Jun 2020 02:00:20: 7000000 INFO @ Tue, 30 Jun 2020 02:00:25: 2000000 INFO @ Tue, 30 Jun 2020 02:00:26: 8000000 INFO @ Tue, 30 Jun 2020 02:00:32: 3000000 INFO @ Tue, 30 Jun 2020 02:00:32: 9000000 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 02:00:39: 10000000 INFO @ Tue, 30 Jun 2020 02:00:39: 4000000 INFO @ Tue, 30 Jun 2020 02:00:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX033324/SRX033324.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX033324/SRX033324.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX033324/SRX033324.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX033324/SRX033324.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 02:00:41: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:00:41: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:00:45: 11000000 INFO @ Tue, 30 Jun 2020 02:00:46: 5000000 INFO @ Tue, 30 Jun 2020 02:00:48: 1000000 INFO @ Tue, 30 Jun 2020 02:00:51: 12000000 INFO @ Tue, 30 Jun 2020 02:00:53: 6000000 INFO @ Tue, 30 Jun 2020 02:00:55: 2000000 INFO @ Tue, 30 Jun 2020 02:00:57: 13000000 INFO @ Tue, 30 Jun 2020 02:01:00: 7000000 INFO @ Tue, 30 Jun 2020 02:01:02: 3000000 INFO @ Tue, 30 Jun 2020 02:01:03: 14000000 INFO @ Tue, 30 Jun 2020 02:01:07: 8000000 INFO @ Tue, 30 Jun 2020 02:01:09: 4000000 INFO @ Tue, 30 Jun 2020 02:01:10: 15000000 INFO @ Tue, 30 Jun 2020 02:01:14: 9000000 INFO @ Tue, 30 Jun 2020 02:01:16: 5000000 INFO @ Tue, 30 Jun 2020 02:01:18: 16000000 INFO @ Tue, 30 Jun 2020 02:01:21: 10000000 INFO @ Tue, 30 Jun 2020 02:01:23: 6000000 INFO @ Tue, 30 Jun 2020 02:01:24: 17000000 INFO @ Tue, 30 Jun 2020 02:01:28: 11000000 INFO @ Tue, 30 Jun 2020 02:01:30: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 02:01:30: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 02:01:30: #1 total tags in treatment: 17865376 INFO @ Tue, 30 Jun 2020 02:01:30: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:01:30: #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 02:01:30: 7000000 INFO @ Tue, 30 Jun 2020 02:01:31: #1 tags after filtering in treatment: 17865369 INFO @ Tue, 30 Jun 2020 02:01:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:01:31: #1 finished! INFO @ Tue, 30 Jun 2020 02:01:31: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:01:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:01:32: #2 number of paired peaks: 162 WARNING @ Tue, 30 Jun 2020 02:01:32: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Tue, 30 Jun 2020 02:01:32: start model_add_line... INFO @ Tue, 30 Jun 2020 02:01:32: start X-correlation... INFO @ Tue, 30 Jun 2020 02:01:32: end of X-cor INFO @ Tue, 30 Jun 2020 02:01:32: #2 finished! INFO @ Tue, 30 Jun 2020 02:01:32: #2 predicted fragment length is 105 bps INFO @ Tue, 30 Jun 2020 02:01:32: #2 alternative fragment length(s) may be 90,105 bps INFO @ Tue, 30 Jun 2020 02:01:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX033324/SRX033324.05_model.r INFO @ Tue, 30 Jun 2020 02:01:32: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:01:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:01:35: 12000000 INFO @ Tue, 30 Jun 2020 02:01:37: 8000000 INFO @ Tue, 30 Jun 2020 02:01:41: 13000000 INFO @ Tue, 30 Jun 2020 02:01:43: 9000000 INFO @ Tue, 30 Jun 2020 02:01:48: 14000000 INFO @ Tue, 30 Jun 2020 02:01:50: 10000000 INFO @ Tue, 30 Jun 2020 02:01:56: 15000000 INFO @ Tue, 30 Jun 2020 02:01:57: 11000000 INFO @ Tue, 30 Jun 2020 02:02:03: 16000000 INFO @ Tue, 30 Jun 2020 02:02:03: 12000000 INFO @ Tue, 30 Jun 2020 02:02:06: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:02:10: 17000000 INFO @ Tue, 30 Jun 2020 02:02:10: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:02:16: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 02:02:16: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 02:02:16: #1 total tags in treatment: 17865376 INFO @ Tue, 30 Jun 2020 02:02:16: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:02:16: #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 02:02:16: 14000000 INFO @ Tue, 30 Jun 2020 02:02:17: #1 tags after filtering in treatment: 17865369 INFO @ Tue, 30 Jun 2020 02:02:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:02:17: #1 finished! INFO @ Tue, 30 Jun 2020 02:02:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:02:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:02:18: #2 number of paired peaks: 162 WARNING @ Tue, 30 Jun 2020 02:02:18: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Tue, 30 Jun 2020 02:02:18: start model_add_line... INFO @ Tue, 30 Jun 2020 02:02:18: start X-correlation... INFO @ Tue, 30 Jun 2020 02:02:18: end of X-cor INFO @ Tue, 30 Jun 2020 02:02:18: #2 finished! INFO @ Tue, 30 Jun 2020 02:02:18: #2 predicted fragment length is 105 bps INFO @ Tue, 30 Jun 2020 02:02:18: #2 alternative fragment length(s) may be 90,105 bps INFO @ Tue, 30 Jun 2020 02:02:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX033324/SRX033324.10_model.r INFO @ Tue, 30 Jun 2020 02:02:18: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:02:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:02:24: 15000000 INFO @ Tue, 30 Jun 2020 02:02:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX033324/SRX033324.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:02:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX033324/SRX033324.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:02:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX033324/SRX033324.05_summits.bed INFO @ Tue, 30 Jun 2020 02:02:24: Done! pass1 - making usageList (391 chroms): 2 millis pass2 - checking and writing primary data (2350 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:02:31: 16000000 INFO @ Tue, 30 Jun 2020 02:02:37: 17000000 INFO @ Tue, 30 Jun 2020 02:02:43: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 02:02:43: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 02:02:43: #1 total tags in treatment: 17865376 INFO @ Tue, 30 Jun 2020 02:02:43: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:02:43: #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 02:02:44: #1 tags after filtering in treatment: 17865369 INFO @ Tue, 30 Jun 2020 02:02:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:02:44: #1 finished! INFO @ Tue, 30 Jun 2020 02:02:44: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:02:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:02:45: #2 number of paired peaks: 162 WARNING @ Tue, 30 Jun 2020 02:02:45: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Tue, 30 Jun 2020 02:02:45: start model_add_line... INFO @ Tue, 30 Jun 2020 02:02:45: start X-correlation... INFO @ Tue, 30 Jun 2020 02:02:45: end of X-cor INFO @ Tue, 30 Jun 2020 02:02:45: #2 finished! INFO @ Tue, 30 Jun 2020 02:02:45: #2 predicted fragment length is 105 bps INFO @ Tue, 30 Jun 2020 02:02:45: #2 alternative fragment length(s) may be 90,105 bps INFO @ Tue, 30 Jun 2020 02:02:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX033324/SRX033324.20_model.r INFO @ Tue, 30 Jun 2020 02:02:45: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:02:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:02:52: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:03:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX033324/SRX033324.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:03:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX033324/SRX033324.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:03:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX033324/SRX033324.10_summits.bed INFO @ Tue, 30 Jun 2020 02:03:10: Done! pass1 - making usageList (192 chroms): 2 millis pass2 - checking and writing primary data (522 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:03:18: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:03:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX033324/SRX033324.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:03:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX033324/SRX033324.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:03:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX033324/SRX033324.20_summits.bed INFO @ Tue, 30 Jun 2020 02:03:37: Done! pass1 - making usageList (87 chroms): 1 millis pass2 - checking and writing primary data (189 records, 4 fields): 7 millis CompletedMACS2peakCalling