Job ID = 6529534 SRX = SRX287985 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: 00:03:24 14627758 reads; of these: 14627758 (100.00%) were unpaired; of these: 1150446 (7.86%) aligned 0 times 12162469 (83.15%) aligned exactly 1 time 1314843 (8.99%) aligned >1 times 92.14% overall alignment rate Time searching: 00:03:24 Overall time: 00:03:24 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] 1217870 / 13477312 = 0.0904 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 02:26:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287985/SRX287985.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287985/SRX287985.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287985/SRX287985.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287985/SRX287985.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 02:26:55: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:26:55: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:27:01: 1000000 INFO @ Tue, 30 Jun 2020 02:27:08: 2000000 INFO @ Tue, 30 Jun 2020 02:27:14: 3000000 INFO @ Tue, 30 Jun 2020 02:27:21: 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 02:27:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287985/SRX287985.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287985/SRX287985.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287985/SRX287985.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287985/SRX287985.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 02:27:27: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:27:27: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:27:28: 5000000 INFO @ Tue, 30 Jun 2020 02:27:35: 1000000 INFO @ Tue, 30 Jun 2020 02:27:36: 6000000 INFO @ Tue, 30 Jun 2020 02:27:44: 7000000 INFO @ Tue, 30 Jun 2020 02:27:44: 2000000 INFO @ Tue, 30 Jun 2020 02:27:52: 8000000 INFO @ Tue, 30 Jun 2020 02:27:52: 3000000 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 02:27:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287985/SRX287985.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287985/SRX287985.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287985/SRX287985.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287985/SRX287985.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 02:27:55: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:27:55: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:28:00: 9000000 INFO @ Tue, 30 Jun 2020 02:28:01: 4000000 INFO @ Tue, 30 Jun 2020 02:28:04: 1000000 INFO @ Tue, 30 Jun 2020 02:28:08: 10000000 INFO @ Tue, 30 Jun 2020 02:28:09: 5000000 INFO @ Tue, 30 Jun 2020 02:28:12: 2000000 INFO @ Tue, 30 Jun 2020 02:28:17: 11000000 INFO @ Tue, 30 Jun 2020 02:28:18: 6000000 INFO @ Tue, 30 Jun 2020 02:28:21: 3000000 INFO @ Tue, 30 Jun 2020 02:28:25: 12000000 INFO @ Tue, 30 Jun 2020 02:28:26: 7000000 INFO @ Tue, 30 Jun 2020 02:28:27: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:28:27: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:28:27: #1 total tags in treatment: 12259442 INFO @ Tue, 30 Jun 2020 02:28:27: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:28:27: #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 02:28:28: #1 tags after filtering in treatment: 12259415 INFO @ Tue, 30 Jun 2020 02:28:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:28:28: #1 finished! INFO @ Tue, 30 Jun 2020 02:28:28: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:28:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:28:29: #2 number of paired peaks: 221 WARNING @ Tue, 30 Jun 2020 02:28:29: Fewer paired peaks (221) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 221 pairs to build model! INFO @ Tue, 30 Jun 2020 02:28:29: start model_add_line... INFO @ Tue, 30 Jun 2020 02:28:29: start X-correlation... INFO @ Tue, 30 Jun 2020 02:28:29: end of X-cor INFO @ Tue, 30 Jun 2020 02:28:29: #2 finished! INFO @ Tue, 30 Jun 2020 02:28:29: #2 predicted fragment length is 136 bps INFO @ Tue, 30 Jun 2020 02:28:29: #2 alternative fragment length(s) may be 136,577,598 bps INFO @ Tue, 30 Jun 2020 02:28:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287985/SRX287985.05_model.r INFO @ Tue, 30 Jun 2020 02:28:29: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:28:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:28:29: 4000000 INFO @ Tue, 30 Jun 2020 02:28:35: 8000000 INFO @ Tue, 30 Jun 2020 02:28:38: 5000000 INFO @ Tue, 30 Jun 2020 02:28:44: 9000000 INFO @ Tue, 30 Jun 2020 02:28:46: 6000000 INFO @ Tue, 30 Jun 2020 02:28:52: 10000000 INFO @ Tue, 30 Jun 2020 02:28:55: 7000000 INFO @ Tue, 30 Jun 2020 02:29:01: 11000000 INFO @ Tue, 30 Jun 2020 02:29:02: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:29:04: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:29:09: 12000000 INFO @ Tue, 30 Jun 2020 02:29:12: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:29:12: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:29:12: #1 total tags in treatment: 12259442 INFO @ Tue, 30 Jun 2020 02:29:12: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:29:12: #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 02:29:12: #1 tags after filtering in treatment: 12259415 INFO @ Tue, 30 Jun 2020 02:29:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:29:12: #1 finished! INFO @ Tue, 30 Jun 2020 02:29:12: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:29:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:29:12: 9000000 INFO @ Tue, 30 Jun 2020 02:29:13: #2 number of paired peaks: 221 WARNING @ Tue, 30 Jun 2020 02:29:13: Fewer paired peaks (221) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 221 pairs to build model! INFO @ Tue, 30 Jun 2020 02:29:13: start model_add_line... INFO @ Tue, 30 Jun 2020 02:29:13: start X-correlation... INFO @ Tue, 30 Jun 2020 02:29:13: end of X-cor INFO @ Tue, 30 Jun 2020 02:29:13: #2 finished! INFO @ Tue, 30 Jun 2020 02:29:13: #2 predicted fragment length is 136 bps INFO @ Tue, 30 Jun 2020 02:29:13: #2 alternative fragment length(s) may be 136,577,598 bps INFO @ Tue, 30 Jun 2020 02:29:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287985/SRX287985.10_model.r INFO @ Tue, 30 Jun 2020 02:29:13: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:29:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:29:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287985/SRX287985.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:29:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287985/SRX287985.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:29:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287985/SRX287985.05_summits.bed INFO @ Tue, 30 Jun 2020 02:29:19: Done! pass1 - making usageList (133 chroms): 1 millis pass2 - checking and writing primary data (3212 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:29:20: 10000000 INFO @ Tue, 30 Jun 2020 02:29:29: 11000000 INFO @ Tue, 30 Jun 2020 02:29:36: 12000000 INFO @ Tue, 30 Jun 2020 02:29:38: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:29:38: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:29:38: #1 total tags in treatment: 12259442 INFO @ Tue, 30 Jun 2020 02:29:38: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:29:38: #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 02:29:39: #1 tags after filtering in treatment: 12259415 INFO @ Tue, 30 Jun 2020 02:29:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:29:39: #1 finished! INFO @ Tue, 30 Jun 2020 02:29:39: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:29:39: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:29:40: #2 number of paired peaks: 221 WARNING @ Tue, 30 Jun 2020 02:29:40: Fewer paired peaks (221) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 221 pairs to build model! INFO @ Tue, 30 Jun 2020 02:29:40: start model_add_line... INFO @ Tue, 30 Jun 2020 02:29:40: start X-correlation... INFO @ Tue, 30 Jun 2020 02:29:40: end of X-cor INFO @ Tue, 30 Jun 2020 02:29:40: #2 finished! INFO @ Tue, 30 Jun 2020 02:29:40: #2 predicted fragment length is 136 bps INFO @ Tue, 30 Jun 2020 02:29:40: #2 alternative fragment length(s) may be 136,577,598 bps INFO @ Tue, 30 Jun 2020 02:29:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287985/SRX287985.20_model.r INFO @ Tue, 30 Jun 2020 02:29:40: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:29:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:29:44: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:29:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287985/SRX287985.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:29:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287985/SRX287985.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:29:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287985/SRX287985.10_summits.bed INFO @ Tue, 30 Jun 2020 02:29:59: Done! pass1 - making usageList (75 chroms): 1 millis pass2 - checking and writing primary data (1068 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:30:10: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:30:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287985/SRX287985.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:30:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287985/SRX287985.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:30:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287985/SRX287985.20_summits.bed INFO @ Tue, 30 Jun 2020 02:30:25: Done! pass1 - making usageList (52 chroms): 1 millis pass2 - checking and writing primary data (153 records, 4 fields): 4 millis CompletedMACS2peakCalling