Job ID = 6529285 SRX = SRX124475 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: 00:00:43 3788985 reads; of these: 3788985 (100.00%) were unpaired; of these: 155811 (4.11%) aligned 0 times 2816730 (74.34%) aligned exactly 1 time 816444 (21.55%) aligned >1 times 95.89% overall alignment rate Time searching: 00:00:43 Overall time: 00:00:43 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_rmdupse_core] 131911 / 3633174 = 0.0363 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 02:01:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX124475/SRX124475.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX124475/SRX124475.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX124475/SRX124475.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX124475/SRX124475.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 02:01:03: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:01:03: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:01:09: 1000000 INFO @ Tue, 30 Jun 2020 02:01:15: 2000000 INFO @ Tue, 30 Jun 2020 02:01:21: 3000000 INFO @ Tue, 30 Jun 2020 02:01:24: #1 tag size is determined as 30 bps INFO @ Tue, 30 Jun 2020 02:01:24: #1 tag size = 30 INFO @ Tue, 30 Jun 2020 02:01:24: #1 total tags in treatment: 3501263 INFO @ Tue, 30 Jun 2020 02:01:24: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:01:24: #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 02:01:24: #1 tags after filtering in treatment: 3501202 INFO @ Tue, 30 Jun 2020 02:01:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:01:24: #1 finished! INFO @ Tue, 30 Jun 2020 02:01:24: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:01:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:01:24: #2 number of paired peaks: 396 WARNING @ Tue, 30 Jun 2020 02:01:24: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Tue, 30 Jun 2020 02:01:24: start model_add_line... INFO @ Tue, 30 Jun 2020 02:01:24: start X-correlation... INFO @ Tue, 30 Jun 2020 02:01:24: end of X-cor INFO @ Tue, 30 Jun 2020 02:01:24: #2 finished! INFO @ Tue, 30 Jun 2020 02:01:24: #2 predicted fragment length is 65 bps INFO @ Tue, 30 Jun 2020 02:01:24: #2 alternative fragment length(s) may be 65,528 bps INFO @ Tue, 30 Jun 2020 02:01:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX124475/SRX124475.05_model.r INFO @ Tue, 30 Jun 2020 02:01:25: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:01:25: #3 Pre-compute pvalue-qvalue table... 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 02:01:33: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:01:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX124475/SRX124475.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX124475/SRX124475.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX124475/SRX124475.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX124475/SRX124475.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 02:01:34: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:01:34: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:01:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX124475/SRX124475.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:01:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX124475/SRX124475.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:01:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX124475/SRX124475.05_summits.bed INFO @ Tue, 30 Jun 2020 02:01:37: Done! pass1 - making usageList (180 chroms): 1 millis pass2 - checking and writing primary data (422 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:01:40: 1000000 INFO @ Tue, 30 Jun 2020 02:01:46: 2000000 INFO @ Tue, 30 Jun 2020 02:01:53: 3000000 INFO @ Tue, 30 Jun 2020 02:01:56: #1 tag size is determined as 30 bps INFO @ Tue, 30 Jun 2020 02:01:56: #1 tag size = 30 INFO @ Tue, 30 Jun 2020 02:01:56: #1 total tags in treatment: 3501263 INFO @ Tue, 30 Jun 2020 02:01:56: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:01:56: #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 02:01:56: #1 tags after filtering in treatment: 3501202 INFO @ Tue, 30 Jun 2020 02:01:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:01:56: #1 finished! INFO @ Tue, 30 Jun 2020 02:01:56: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:01:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:01:56: #2 number of paired peaks: 396 WARNING @ Tue, 30 Jun 2020 02:01:56: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Tue, 30 Jun 2020 02:01:56: start model_add_line... INFO @ Tue, 30 Jun 2020 02:01:57: start X-correlation... INFO @ Tue, 30 Jun 2020 02:01:57: end of X-cor INFO @ Tue, 30 Jun 2020 02:01:57: #2 finished! INFO @ Tue, 30 Jun 2020 02:01:57: #2 predicted fragment length is 65 bps INFO @ Tue, 30 Jun 2020 02:01:57: #2 alternative fragment length(s) may be 65,528 bps INFO @ Tue, 30 Jun 2020 02:01:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX124475/SRX124475.10_model.r INFO @ Tue, 30 Jun 2020 02:01:57: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:01:57: #3 Pre-compute pvalue-qvalue table... 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 02:02:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX124475/SRX124475.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX124475/SRX124475.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX124475/SRX124475.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX124475/SRX124475.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 02:02:03: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:02:03: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:02:05: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:02:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX124475/SRX124475.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:02:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX124475/SRX124475.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:02:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX124475/SRX124475.10_summits.bed INFO @ Tue, 30 Jun 2020 02:02:09: Done! pass1 - making usageList (100 chroms): 1 millis pass2 - checking and writing primary data (212 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:02:10: 1000000 INFO @ Tue, 30 Jun 2020 02:02:16: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:02:23: 3000000 INFO @ Tue, 30 Jun 2020 02:02:26: #1 tag size is determined as 30 bps INFO @ Tue, 30 Jun 2020 02:02:26: #1 tag size = 30 INFO @ Tue, 30 Jun 2020 02:02:26: #1 total tags in treatment: 3501263 INFO @ Tue, 30 Jun 2020 02:02:26: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:02:26: #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 02:02:26: #1 tags after filtering in treatment: 3501202 INFO @ Tue, 30 Jun 2020 02:02:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:02:26: #1 finished! INFO @ Tue, 30 Jun 2020 02:02:26: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:02:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:02:27: #2 number of paired peaks: 396 WARNING @ Tue, 30 Jun 2020 02:02:27: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Tue, 30 Jun 2020 02:02:27: start model_add_line... INFO @ Tue, 30 Jun 2020 02:02:27: start X-correlation... INFO @ Tue, 30 Jun 2020 02:02:27: end of X-cor INFO @ Tue, 30 Jun 2020 02:02:27: #2 finished! INFO @ Tue, 30 Jun 2020 02:02:27: #2 predicted fragment length is 65 bps INFO @ Tue, 30 Jun 2020 02:02:27: #2 alternative fragment length(s) may be 65,528 bps INFO @ Tue, 30 Jun 2020 02:02:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX124475/SRX124475.20_model.r INFO @ Tue, 30 Jun 2020 02:02:27: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:02:27: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:02:35: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:02:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX124475/SRX124475.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:02:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX124475/SRX124475.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:02:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX124475/SRX124475.20_summits.bed INFO @ Tue, 30 Jun 2020 02:02:40: Done! pass1 - making usageList (65 chroms): 2 millis pass2 - checking and writing primary data (111 records, 4 fields): 2 millis CompletedMACS2peakCalling