Job ID = 6529719 SRX = SRX4158195 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: 00:04:41 19568830 reads; of these: 19568830 (100.00%) were unpaired; of these: 680337 (3.48%) aligned 0 times 17113562 (87.45%) aligned exactly 1 time 1774931 (9.07%) aligned >1 times 96.52% overall alignment rate Time searching: 00:04:41 Overall time: 00:04:41 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] 1890688 / 18888493 = 0.1001 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 02:57:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4158195/SRX4158195.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4158195/SRX4158195.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4158195/SRX4158195.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4158195/SRX4158195.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 02:57:09: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:57:09: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:57:15: 1000000 INFO @ Tue, 30 Jun 2020 02:57:21: 2000000 INFO @ Tue, 30 Jun 2020 02:57:27: 3000000 INFO @ Tue, 30 Jun 2020 02:57:33: 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 02:57:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4158195/SRX4158195.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4158195/SRX4158195.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4158195/SRX4158195.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4158195/SRX4158195.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 02:57:39: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:57:39: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:57:40: 5000000 INFO @ Tue, 30 Jun 2020 02:57:45: 1000000 INFO @ Tue, 30 Jun 2020 02:57:46: 6000000 INFO @ Tue, 30 Jun 2020 02:57:52: 2000000 INFO @ Tue, 30 Jun 2020 02:57:53: 7000000 INFO @ Tue, 30 Jun 2020 02:57:59: 3000000 INFO @ Tue, 30 Jun 2020 02:58:00: 8000000 INFO @ Tue, 30 Jun 2020 02:58:06: 4000000 INFO @ Tue, 30 Jun 2020 02:58:06: 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 02:58:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4158195/SRX4158195.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4158195/SRX4158195.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4158195/SRX4158195.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4158195/SRX4158195.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 02:58:09: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:58:09: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:58:13: 10000000 INFO @ Tue, 30 Jun 2020 02:58:13: 5000000 INFO @ Tue, 30 Jun 2020 02:58:16: 1000000 INFO @ Tue, 30 Jun 2020 02:58:19: 11000000 INFO @ Tue, 30 Jun 2020 02:58:20: 6000000 INFO @ Tue, 30 Jun 2020 02:58:23: 2000000 INFO @ Tue, 30 Jun 2020 02:58:26: 12000000 INFO @ Tue, 30 Jun 2020 02:58:27: 7000000 INFO @ Tue, 30 Jun 2020 02:58:30: 3000000 INFO @ Tue, 30 Jun 2020 02:58:33: 13000000 INFO @ Tue, 30 Jun 2020 02:58:34: 8000000 INFO @ Tue, 30 Jun 2020 02:58:38: 4000000 INFO @ Tue, 30 Jun 2020 02:58:40: 14000000 INFO @ Tue, 30 Jun 2020 02:58:41: 9000000 INFO @ Tue, 30 Jun 2020 02:58:45: 5000000 INFO @ Tue, 30 Jun 2020 02:58:47: 15000000 INFO @ Tue, 30 Jun 2020 02:58:48: 10000000 INFO @ Tue, 30 Jun 2020 02:58:52: 6000000 INFO @ Tue, 30 Jun 2020 02:58:54: 16000000 INFO @ Tue, 30 Jun 2020 02:58:55: 11000000 INFO @ Tue, 30 Jun 2020 02:58:59: 7000000 INFO @ Tue, 30 Jun 2020 02:59:01: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:59:01: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:59:01: #1 total tags in treatment: 16997805 INFO @ Tue, 30 Jun 2020 02:59:01: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:59:01: #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 02:59:02: #1 tags after filtering in treatment: 16997617 INFO @ Tue, 30 Jun 2020 02:59:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:59:02: #1 finished! INFO @ Tue, 30 Jun 2020 02:59:02: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:59:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:59:03: 12000000 INFO @ Tue, 30 Jun 2020 02:59:03: #2 number of paired peaks: 126 WARNING @ Tue, 30 Jun 2020 02:59:03: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Tue, 30 Jun 2020 02:59:03: start model_add_line... INFO @ Tue, 30 Jun 2020 02:59:03: start X-correlation... INFO @ Tue, 30 Jun 2020 02:59:03: end of X-cor INFO @ Tue, 30 Jun 2020 02:59:03: #2 finished! INFO @ Tue, 30 Jun 2020 02:59:03: #2 predicted fragment length is 137 bps INFO @ Tue, 30 Jun 2020 02:59:03: #2 alternative fragment length(s) may be 137 bps INFO @ Tue, 30 Jun 2020 02:59:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4158195/SRX4158195.05_model.r INFO @ Tue, 30 Jun 2020 02:59:03: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:59:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:59:06: 8000000 INFO @ Tue, 30 Jun 2020 02:59:10: 13000000 INFO @ Tue, 30 Jun 2020 02:59:12: 9000000 INFO @ Tue, 30 Jun 2020 02:59:18: 14000000 INFO @ Tue, 30 Jun 2020 02:59:19: 10000000 INFO @ Tue, 30 Jun 2020 02:59:25: 15000000 INFO @ Tue, 30 Jun 2020 02:59:26: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:59:32: 16000000 INFO @ Tue, 30 Jun 2020 02:59:33: 12000000 INFO @ Tue, 30 Jun 2020 02:59:40: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:59:40: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:59:40: #1 total tags in treatment: 16997805 INFO @ Tue, 30 Jun 2020 02:59:40: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:59:40: #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 02:59:40: 13000000 INFO @ Tue, 30 Jun 2020 02:59:40: #1 tags after filtering in treatment: 16997617 INFO @ Tue, 30 Jun 2020 02:59:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:59:40: #1 finished! INFO @ Tue, 30 Jun 2020 02:59:40: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:59:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:59:41: #2 number of paired peaks: 126 WARNING @ Tue, 30 Jun 2020 02:59:41: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Tue, 30 Jun 2020 02:59:41: start model_add_line... INFO @ Tue, 30 Jun 2020 02:59:41: start X-correlation... INFO @ Tue, 30 Jun 2020 02:59:42: end of X-cor INFO @ Tue, 30 Jun 2020 02:59:42: #2 finished! INFO @ Tue, 30 Jun 2020 02:59:42: #2 predicted fragment length is 137 bps INFO @ Tue, 30 Jun 2020 02:59:42: #2 alternative fragment length(s) may be 137 bps INFO @ Tue, 30 Jun 2020 02:59:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4158195/SRX4158195.10_model.r INFO @ Tue, 30 Jun 2020 02:59:42: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:59:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:59:43: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:59:47: 14000000 INFO @ Tue, 30 Jun 2020 02:59:53: 15000000 INFO @ Tue, 30 Jun 2020 02:59:59: 16000000 INFO @ Tue, 30 Jun 2020 03:00:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4158195/SRX4158195.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:00:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4158195/SRX4158195.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:00:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4158195/SRX4158195.05_summits.bed INFO @ Tue, 30 Jun 2020 03:00:03: Done! pass1 - making usageList (130 chroms): 2 millis pass2 - checking and writing primary data (13664 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:00:06: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:00:06: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:00:06: #1 total tags in treatment: 16997805 INFO @ Tue, 30 Jun 2020 03:00:06: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:00:06: #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 03:00:07: #1 tags after filtering in treatment: 16997617 INFO @ Tue, 30 Jun 2020 03:00:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:00:07: #1 finished! INFO @ Tue, 30 Jun 2020 03:00:07: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:00:07: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:00:08: #2 number of paired peaks: 126 WARNING @ Tue, 30 Jun 2020 03:00:08: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Tue, 30 Jun 2020 03:00:08: start model_add_line... INFO @ Tue, 30 Jun 2020 03:00:08: start X-correlation... INFO @ Tue, 30 Jun 2020 03:00:08: end of X-cor INFO @ Tue, 30 Jun 2020 03:00:08: #2 finished! INFO @ Tue, 30 Jun 2020 03:00:08: #2 predicted fragment length is 137 bps INFO @ Tue, 30 Jun 2020 03:00:08: #2 alternative fragment length(s) may be 137 bps INFO @ Tue, 30 Jun 2020 03:00:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4158195/SRX4158195.20_model.r INFO @ Tue, 30 Jun 2020 03:00:08: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:00:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:00:23: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:00:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4158195/SRX4158195.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:00:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4158195/SRX4158195.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:00:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4158195/SRX4158195.10_summits.bed INFO @ Tue, 30 Jun 2020 03:00:45: Done! pass1 - making usageList (80 chroms): 1 millis pass2 - checking and writing primary data (2330 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:00:46: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:01:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4158195/SRX4158195.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:01:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4158195/SRX4158195.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:01:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4158195/SRX4158195.20_summits.bed INFO @ Tue, 30 Jun 2020 03:01:07: Done! pass1 - making usageList (56 chroms): 1 millis pass2 - checking and writing primary data (249 records, 4 fields): 4 millis CompletedMACS2peakCalling