Job ID = 6529188 SRX = SRX033314 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:40 23969437 reads; of these: 23969437 (100.00%) were unpaired; of these: 813877 (3.40%) aligned 0 times 20119363 (83.94%) aligned exactly 1 time 3036197 (12.67%) aligned >1 times 96.60% 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] 3736611 / 23155560 = 0.1614 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 01:51:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX033314/SRX033314.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX033314/SRX033314.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX033314/SRX033314.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX033314/SRX033314.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 01:51:10: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:51:10: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:51:16: 1000000 INFO @ Tue, 30 Jun 2020 01:51:23: 2000000 INFO @ Tue, 30 Jun 2020 01:51:29: 3000000 INFO @ Tue, 30 Jun 2020 01:51:35: 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 01:51:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX033314/SRX033314.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX033314/SRX033314.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX033314/SRX033314.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX033314/SRX033314.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 01:51:40: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:51:40: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:51:42: 5000000 INFO @ Tue, 30 Jun 2020 01:51:47: 1000000 INFO @ Tue, 30 Jun 2020 01:51:49: 6000000 INFO @ Tue, 30 Jun 2020 01:51:54: 2000000 INFO @ Tue, 30 Jun 2020 01:51:56: 7000000 INFO @ Tue, 30 Jun 2020 01:52:01: 3000000 INFO @ Tue, 30 Jun 2020 01:52:02: 8000000 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 01:52:08: 4000000 INFO @ Tue, 30 Jun 2020 01:52:09: 9000000 INFO @ Tue, 30 Jun 2020 01:52:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX033314/SRX033314.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX033314/SRX033314.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX033314/SRX033314.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX033314/SRX033314.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 01:52:10: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:52:10: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:52:15: 5000000 INFO @ Tue, 30 Jun 2020 01:52:16: 1000000 INFO @ Tue, 30 Jun 2020 01:52:16: 10000000 INFO @ Tue, 30 Jun 2020 01:52:22: 6000000 INFO @ Tue, 30 Jun 2020 01:52:22: 2000000 INFO @ Tue, 30 Jun 2020 01:52:24: 11000000 INFO @ Tue, 30 Jun 2020 01:52:29: 3000000 INFO @ Tue, 30 Jun 2020 01:52:29: 7000000 INFO @ Tue, 30 Jun 2020 01:52:31: 12000000 INFO @ Tue, 30 Jun 2020 01:52:35: 4000000 INFO @ Tue, 30 Jun 2020 01:52:36: 8000000 INFO @ Tue, 30 Jun 2020 01:52:38: 13000000 INFO @ Tue, 30 Jun 2020 01:52:42: 5000000 INFO @ Tue, 30 Jun 2020 01:52:43: 9000000 INFO @ Tue, 30 Jun 2020 01:52:45: 14000000 INFO @ Tue, 30 Jun 2020 01:52:48: 6000000 INFO @ Tue, 30 Jun 2020 01:52:50: 10000000 INFO @ Tue, 30 Jun 2020 01:52:52: 15000000 INFO @ Tue, 30 Jun 2020 01:52:55: 7000000 INFO @ Tue, 30 Jun 2020 01:52:57: 11000000 INFO @ Tue, 30 Jun 2020 01:53:00: 16000000 INFO @ Tue, 30 Jun 2020 01:53:01: 8000000 INFO @ Tue, 30 Jun 2020 01:53:04: 12000000 INFO @ Tue, 30 Jun 2020 01:53:07: 17000000 INFO @ Tue, 30 Jun 2020 01:53:08: 9000000 INFO @ Tue, 30 Jun 2020 01:53:12: 13000000 INFO @ Tue, 30 Jun 2020 01:53:14: 10000000 INFO @ Tue, 30 Jun 2020 01:53:14: 18000000 INFO @ Tue, 30 Jun 2020 01:53:19: 14000000 INFO @ Tue, 30 Jun 2020 01:53:20: 11000000 INFO @ Tue, 30 Jun 2020 01:53:22: 19000000 INFO @ Tue, 30 Jun 2020 01:53:25: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:53:25: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:53:25: #1 total tags in treatment: 19418949 INFO @ Tue, 30 Jun 2020 01:53:25: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:53:25: #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 01:53:26: #1 tags after filtering in treatment: 19418925 INFO @ Tue, 30 Jun 2020 01:53:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:53:26: #1 finished! INFO @ Tue, 30 Jun 2020 01:53:26: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:53:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:53:26: 15000000 INFO @ Tue, 30 Jun 2020 01:53:26: 12000000 INFO @ Tue, 30 Jun 2020 01:53:27: #2 number of paired peaks: 115 WARNING @ Tue, 30 Jun 2020 01:53:27: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Tue, 30 Jun 2020 01:53:27: start model_add_line... INFO @ Tue, 30 Jun 2020 01:53:27: start X-correlation... INFO @ Tue, 30 Jun 2020 01:53:28: end of X-cor INFO @ Tue, 30 Jun 2020 01:53:28: #2 finished! INFO @ Tue, 30 Jun 2020 01:53:28: #2 predicted fragment length is 163 bps INFO @ Tue, 30 Jun 2020 01:53:28: #2 alternative fragment length(s) may be 163 bps INFO @ Tue, 30 Jun 2020 01:53:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX033314/SRX033314.05_model.r INFO @ Tue, 30 Jun 2020 01:53:28: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:53:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:53:33: 13000000 INFO @ Tue, 30 Jun 2020 01:53:34: 16000000 INFO @ Tue, 30 Jun 2020 01:53:39: 14000000 INFO @ Tue, 30 Jun 2020 01:53:41: 17000000 INFO @ Tue, 30 Jun 2020 01:53:46: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:53:48: 18000000 INFO @ Tue, 30 Jun 2020 01:53:53: 16000000 INFO @ Tue, 30 Jun 2020 01:53:54: 19000000 INFO @ Tue, 30 Jun 2020 01:53:58: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:53:58: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:53:58: #1 total tags in treatment: 19418949 INFO @ Tue, 30 Jun 2020 01:53:58: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:53:58: #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 01:53:59: #1 tags after filtering in treatment: 19418925 INFO @ Tue, 30 Jun 2020 01:53:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:53:59: #1 finished! INFO @ Tue, 30 Jun 2020 01:53:59: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:53:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:53:59: 17000000 INFO @ Tue, 30 Jun 2020 01:54:00: #2 number of paired peaks: 115 WARNING @ Tue, 30 Jun 2020 01:54:00: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Tue, 30 Jun 2020 01:54:00: start model_add_line... INFO @ Tue, 30 Jun 2020 01:54:00: start X-correlation... INFO @ Tue, 30 Jun 2020 01:54:00: end of X-cor INFO @ Tue, 30 Jun 2020 01:54:00: #2 finished! INFO @ Tue, 30 Jun 2020 01:54:00: #2 predicted fragment length is 163 bps INFO @ Tue, 30 Jun 2020 01:54:00: #2 alternative fragment length(s) may be 163 bps INFO @ Tue, 30 Jun 2020 01:54:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX033314/SRX033314.10_model.r INFO @ Tue, 30 Jun 2020 01:54:00: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:54:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:54:05: 18000000 INFO @ Tue, 30 Jun 2020 01:54:07: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:54:11: 19000000 INFO @ Tue, 30 Jun 2020 01:54:14: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:54:14: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:54:14: #1 total tags in treatment: 19418949 INFO @ Tue, 30 Jun 2020 01:54:14: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:54:14: #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 01:54:15: #1 tags after filtering in treatment: 19418925 INFO @ Tue, 30 Jun 2020 01:54:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:54:15: #1 finished! INFO @ Tue, 30 Jun 2020 01:54:15: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:54:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:54:17: #2 number of paired peaks: 115 WARNING @ Tue, 30 Jun 2020 01:54:17: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Tue, 30 Jun 2020 01:54:17: start model_add_line... INFO @ Tue, 30 Jun 2020 01:54:17: start X-correlation... INFO @ Tue, 30 Jun 2020 01:54:17: end of X-cor INFO @ Tue, 30 Jun 2020 01:54:17: #2 finished! INFO @ Tue, 30 Jun 2020 01:54:17: #2 predicted fragment length is 163 bps INFO @ Tue, 30 Jun 2020 01:54:17: #2 alternative fragment length(s) may be 163 bps INFO @ Tue, 30 Jun 2020 01:54:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX033314/SRX033314.20_model.r INFO @ Tue, 30 Jun 2020 01:54:17: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:54:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:54:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX033314/SRX033314.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:54:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX033314/SRX033314.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:54:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX033314/SRX033314.05_summits.bed INFO @ Tue, 30 Jun 2020 01:54:29: Done! pass1 - making usageList (193 chroms): 3 millis pass2 - checking and writing primary data (10941 records, 4 fields): 23 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:54:39: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:54:56: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:55:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX033314/SRX033314.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:55:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX033314/SRX033314.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:55:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX033314/SRX033314.10_summits.bed INFO @ Tue, 30 Jun 2020 01:55:00: Done! pass1 - making usageList (100 chroms): 2 millis pass2 - checking and writing primary data (4221 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:55:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX033314/SRX033314.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:55:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX033314/SRX033314.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:55:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX033314/SRX033314.20_summits.bed INFO @ Tue, 30 Jun 2020 01:55:17: Done! pass1 - making usageList (53 chroms): 1 millis pass2 - checking and writing primary data (983 records, 4 fields): 5 millis CompletedMACS2peakCalling