Job ID = 8069967 SRX = SRX7191474 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: 00:04:16 17112053 reads; of these: 17112053 (100.00%) were unpaired; of these: 869568 (5.08%) aligned 0 times 12561658 (73.41%) aligned exactly 1 time 3680827 (21.51%) aligned >1 times 94.92% overall alignment rate Time searching: 00:04:16 Overall time: 00:04:16 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] 1583365 / 16242485 = 0.0975 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 @ Sat, 08 Aug 2020 13:07:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7191474/SRX7191474.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7191474/SRX7191474.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7191474/SRX7191474.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7191474/SRX7191474.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 @ Sat, 08 Aug 2020 13:07:39: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:07:39: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:07:45: 1000000 INFO @ Sat, 08 Aug 2020 13:07:51: 2000000 INFO @ Sat, 08 Aug 2020 13:07:57: 3000000 INFO @ Sat, 08 Aug 2020 13:08:02: 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 @ Sat, 08 Aug 2020 13:08:08: 5000000 INFO @ Sat, 08 Aug 2020 13:08:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7191474/SRX7191474.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7191474/SRX7191474.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7191474/SRX7191474.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7191474/SRX7191474.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 @ Sat, 08 Aug 2020 13:08:09: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:08:09: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:08:15: 6000000 INFO @ Sat, 08 Aug 2020 13:08:16: 1000000 INFO @ Sat, 08 Aug 2020 13:08:22: 7000000 INFO @ Sat, 08 Aug 2020 13:08:23: 2000000 INFO @ Sat, 08 Aug 2020 13:08:28: 8000000 INFO @ Sat, 08 Aug 2020 13:08:30: 3000000 INFO @ Sat, 08 Aug 2020 13:08:35: 9000000 INFO @ Sat, 08 Aug 2020 13:08:37: 4000000 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 @ Sat, 08 Aug 2020 13:08:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7191474/SRX7191474.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7191474/SRX7191474.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7191474/SRX7191474.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7191474/SRX7191474.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 @ Sat, 08 Aug 2020 13:08:39: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:08:39: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:08:42: 10000000 INFO @ Sat, 08 Aug 2020 13:08:44: 5000000 INFO @ Sat, 08 Aug 2020 13:08:46: 1000000 INFO @ Sat, 08 Aug 2020 13:08:49: 11000000 INFO @ Sat, 08 Aug 2020 13:08:51: 6000000 INFO @ Sat, 08 Aug 2020 13:08:53: 2000000 INFO @ Sat, 08 Aug 2020 13:08:56: 12000000 INFO @ Sat, 08 Aug 2020 13:08:58: 7000000 INFO @ Sat, 08 Aug 2020 13:08:59: 3000000 INFO @ Sat, 08 Aug 2020 13:09:03: 13000000 INFO @ Sat, 08 Aug 2020 13:09:05: 8000000 INFO @ Sat, 08 Aug 2020 13:09:06: 4000000 INFO @ Sat, 08 Aug 2020 13:09:10: 14000000 INFO @ Sat, 08 Aug 2020 13:09:13: 9000000 INFO @ Sat, 08 Aug 2020 13:09:13: 5000000 INFO @ Sat, 08 Aug 2020 13:09:14: #1 tag size is determined as 50 bps INFO @ Sat, 08 Aug 2020 13:09:14: #1 tag size = 50 INFO @ Sat, 08 Aug 2020 13:09:14: #1 total tags in treatment: 14659120 INFO @ Sat, 08 Aug 2020 13:09:14: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:09:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:09:15: #1 tags after filtering in treatment: 14659118 INFO @ Sat, 08 Aug 2020 13:09:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Aug 2020 13:09:15: #1 finished! INFO @ Sat, 08 Aug 2020 13:09:15: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:09:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:09:16: #2 number of paired peaks: 871 WARNING @ Sat, 08 Aug 2020 13:09:16: Fewer paired peaks (871) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 871 pairs to build model! INFO @ Sat, 08 Aug 2020 13:09:16: start model_add_line... INFO @ Sat, 08 Aug 2020 13:09:16: start X-correlation... INFO @ Sat, 08 Aug 2020 13:09:16: end of X-cor INFO @ Sat, 08 Aug 2020 13:09:16: #2 finished! INFO @ Sat, 08 Aug 2020 13:09:16: #2 predicted fragment length is 182 bps INFO @ Sat, 08 Aug 2020 13:09:16: #2 alternative fragment length(s) may be 182 bps INFO @ Sat, 08 Aug 2020 13:09:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7191474/SRX7191474.05_model.r INFO @ Sat, 08 Aug 2020 13:09:16: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:09:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:09:20: 10000000 INFO @ Sat, 08 Aug 2020 13:09:20: 6000000 INFO @ Sat, 08 Aug 2020 13:09:27: 7000000 INFO @ Sat, 08 Aug 2020 13:09:27: 11000000 INFO @ Sat, 08 Aug 2020 13:09:33: 8000000 INFO @ Sat, 08 Aug 2020 13:09:35: 12000000 INFO @ Sat, 08 Aug 2020 13:09:40: 9000000 INFO @ Sat, 08 Aug 2020 13:09:42: 13000000 INFO @ Sat, 08 Aug 2020 13:09:47: 10000000 INFO @ Sat, 08 Aug 2020 13:09:49: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:09:50: 14000000 INFO @ Sat, 08 Aug 2020 13:09:53: 11000000 INFO @ Sat, 08 Aug 2020 13:09:55: #1 tag size is determined as 50 bps INFO @ Sat, 08 Aug 2020 13:09:55: #1 tag size = 50 INFO @ Sat, 08 Aug 2020 13:09:55: #1 total tags in treatment: 14659120 INFO @ Sat, 08 Aug 2020 13:09:55: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:09:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:09:55: #1 tags after filtering in treatment: 14659118 INFO @ Sat, 08 Aug 2020 13:09:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Aug 2020 13:09:55: #1 finished! INFO @ Sat, 08 Aug 2020 13:09:55: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:09:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:09:56: #2 number of paired peaks: 871 WARNING @ Sat, 08 Aug 2020 13:09:56: Fewer paired peaks (871) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 871 pairs to build model! INFO @ Sat, 08 Aug 2020 13:09:56: start model_add_line... INFO @ Sat, 08 Aug 2020 13:09:56: start X-correlation... INFO @ Sat, 08 Aug 2020 13:09:56: end of X-cor INFO @ Sat, 08 Aug 2020 13:09:56: #2 finished! INFO @ Sat, 08 Aug 2020 13:09:56: #2 predicted fragment length is 182 bps INFO @ Sat, 08 Aug 2020 13:09:56: #2 alternative fragment length(s) may be 182 bps INFO @ Sat, 08 Aug 2020 13:09:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7191474/SRX7191474.10_model.r INFO @ Sat, 08 Aug 2020 13:09:56: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:09:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:10:00: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:10:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7191474/SRX7191474.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:10:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7191474/SRX7191474.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:10:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7191474/SRX7191474.05_summits.bed INFO @ Sat, 08 Aug 2020 13:10:05: Done! pass1 - making usageList (629 chroms): 2 millis pass2 - checking and writing primary data (6644 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:10:06: 13000000 INFO @ Sat, 08 Aug 2020 13:10:11: 14000000 INFO @ Sat, 08 Aug 2020 13:10:15: #1 tag size is determined as 50 bps INFO @ Sat, 08 Aug 2020 13:10:15: #1 tag size = 50 INFO @ Sat, 08 Aug 2020 13:10:15: #1 total tags in treatment: 14659120 INFO @ Sat, 08 Aug 2020 13:10:15: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:10:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:10:16: #1 tags after filtering in treatment: 14659118 INFO @ Sat, 08 Aug 2020 13:10:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Aug 2020 13:10:16: #1 finished! INFO @ Sat, 08 Aug 2020 13:10:16: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:10:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:10:17: #2 number of paired peaks: 871 WARNING @ Sat, 08 Aug 2020 13:10:17: Fewer paired peaks (871) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 871 pairs to build model! INFO @ Sat, 08 Aug 2020 13:10:17: start model_add_line... INFO @ Sat, 08 Aug 2020 13:10:17: start X-correlation... INFO @ Sat, 08 Aug 2020 13:10:17: end of X-cor INFO @ Sat, 08 Aug 2020 13:10:17: #2 finished! INFO @ Sat, 08 Aug 2020 13:10:17: #2 predicted fragment length is 182 bps INFO @ Sat, 08 Aug 2020 13:10:17: #2 alternative fragment length(s) may be 182 bps INFO @ Sat, 08 Aug 2020 13:10:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7191474/SRX7191474.20_model.r INFO @ Sat, 08 Aug 2020 13:10:17: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:10:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:10:25: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:10:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7191474/SRX7191474.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:10:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7191474/SRX7191474.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:10:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7191474/SRX7191474.10_summits.bed INFO @ Sat, 08 Aug 2020 13:10:39: Done! pass1 - making usageList (557 chroms): 2 millis pass2 - checking and writing primary data (4479 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:10:49: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:11:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7191474/SRX7191474.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:11:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7191474/SRX7191474.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:11:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7191474/SRX7191474.20_summits.bed INFO @ Sat, 08 Aug 2020 13:11:04: Done! pass1 - making usageList (400 chroms): 1 millis pass2 - checking and writing primary data (2492 records, 4 fields): 17 millis CompletedMACS2peakCalling