Job ID = 6529368 SRX = SRX209932 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: 00:02:42 11779768 reads; of these: 11779768 (100.00%) were unpaired; of these: 989878 (8.40%) aligned 0 times 8606090 (73.06%) aligned exactly 1 time 2183800 (18.54%) aligned >1 times 91.60% overall alignment rate Time searching: 00:02:42 Overall time: 00:02:42 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] 2098248 / 10789890 = 0.1945 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 01:47:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX209932/SRX209932.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX209932/SRX209932.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX209932/SRX209932.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX209932/SRX209932.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 01:47:10: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:47:10: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:47:17: 1000000 INFO @ Tue, 30 Jun 2020 01:47:23: 2000000 INFO @ Tue, 30 Jun 2020 01:47:29: 3000000 INFO @ Tue, 30 Jun 2020 01:47:35: 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 01:47:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX209932/SRX209932.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX209932/SRX209932.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX209932/SRX209932.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX209932/SRX209932.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 01:47:41: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:47:41: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:47:42: 5000000 INFO @ Tue, 30 Jun 2020 01:47:47: 1000000 INFO @ Tue, 30 Jun 2020 01:47:48: 6000000 INFO @ Tue, 30 Jun 2020 01:47:54: 2000000 INFO @ Tue, 30 Jun 2020 01:47:55: 7000000 INFO @ Tue, 30 Jun 2020 01:48:00: 3000000 INFO @ Tue, 30 Jun 2020 01:48:01: 8000000 INFO @ Tue, 30 Jun 2020 01:48:06: #1 tag size is determined as 40 bps INFO @ Tue, 30 Jun 2020 01:48:06: #1 tag size = 40 INFO @ Tue, 30 Jun 2020 01:48:06: #1 total tags in treatment: 8691642 INFO @ Tue, 30 Jun 2020 01:48:06: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:48:06: #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 01:48:06: 4000000 INFO @ Tue, 30 Jun 2020 01:48:06: #1 tags after filtering in treatment: 8691610 INFO @ Tue, 30 Jun 2020 01:48:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:48:06: #1 finished! INFO @ Tue, 30 Jun 2020 01:48:06: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:48:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:48:07: #2 number of paired peaks: 618 WARNING @ Tue, 30 Jun 2020 01:48:07: Fewer paired peaks (618) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 618 pairs to build model! INFO @ Tue, 30 Jun 2020 01:48:07: start model_add_line... INFO @ Tue, 30 Jun 2020 01:48:07: start X-correlation... INFO @ Tue, 30 Jun 2020 01:48:07: end of X-cor INFO @ Tue, 30 Jun 2020 01:48:07: #2 finished! INFO @ Tue, 30 Jun 2020 01:48:07: #2 predicted fragment length is 89 bps INFO @ Tue, 30 Jun 2020 01:48:07: #2 alternative fragment length(s) may be 4,89 bps INFO @ Tue, 30 Jun 2020 01:48:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX209932/SRX209932.05_model.r INFO @ Tue, 30 Jun 2020 01:48:07: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:48:07: #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 01:48:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX209932/SRX209932.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX209932/SRX209932.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX209932/SRX209932.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX209932/SRX209932.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 01:48:10: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:48:10: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:48:12: 5000000 INFO @ Tue, 30 Jun 2020 01:48:17: 1000000 INFO @ Tue, 30 Jun 2020 01:48:18: 6000000 INFO @ Tue, 30 Jun 2020 01:48:24: 2000000 INFO @ Tue, 30 Jun 2020 01:48:25: 7000000 INFO @ Tue, 30 Jun 2020 01:48:28: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:48:30: 3000000 INFO @ Tue, 30 Jun 2020 01:48:31: 8000000 INFO @ Tue, 30 Jun 2020 01:48:36: #1 tag size is determined as 40 bps INFO @ Tue, 30 Jun 2020 01:48:36: #1 tag size = 40 INFO @ Tue, 30 Jun 2020 01:48:36: #1 total tags in treatment: 8691642 INFO @ Tue, 30 Jun 2020 01:48:36: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:48:36: #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 01:48:36: #1 tags after filtering in treatment: 8691610 INFO @ Tue, 30 Jun 2020 01:48:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:48:36: #1 finished! INFO @ Tue, 30 Jun 2020 01:48:36: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:48:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:48:36: 4000000 INFO @ Tue, 30 Jun 2020 01:48:37: #2 number of paired peaks: 618 WARNING @ Tue, 30 Jun 2020 01:48:37: Fewer paired peaks (618) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 618 pairs to build model! INFO @ Tue, 30 Jun 2020 01:48:37: start model_add_line... INFO @ Tue, 30 Jun 2020 01:48:37: start X-correlation... INFO @ Tue, 30 Jun 2020 01:48:37: end of X-cor INFO @ Tue, 30 Jun 2020 01:48:37: #2 finished! INFO @ Tue, 30 Jun 2020 01:48:37: #2 predicted fragment length is 89 bps INFO @ Tue, 30 Jun 2020 01:48:37: #2 alternative fragment length(s) may be 4,89 bps INFO @ Tue, 30 Jun 2020 01:48:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX209932/SRX209932.10_model.r INFO @ Tue, 30 Jun 2020 01:48:37: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:48:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:48:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX209932/SRX209932.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:48:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX209932/SRX209932.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:48:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX209932/SRX209932.05_summits.bed INFO @ Tue, 30 Jun 2020 01:48:39: Done! pass1 - making usageList (546 chroms): 1 millis pass2 - checking and writing primary data (3207 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:48:42: 5000000 INFO @ Tue, 30 Jun 2020 01:48:48: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:48:55: 7000000 INFO @ Tue, 30 Jun 2020 01:48:57: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:49:01: 8000000 INFO @ Tue, 30 Jun 2020 01:49:05: #1 tag size is determined as 40 bps INFO @ Tue, 30 Jun 2020 01:49:05: #1 tag size = 40 INFO @ Tue, 30 Jun 2020 01:49:05: #1 total tags in treatment: 8691642 INFO @ Tue, 30 Jun 2020 01:49:05: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:49:05: #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 01:49:05: #1 tags after filtering in treatment: 8691610 INFO @ Tue, 30 Jun 2020 01:49:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:49:05: #1 finished! INFO @ Tue, 30 Jun 2020 01:49:05: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:49:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:49:06: #2 number of paired peaks: 618 WARNING @ Tue, 30 Jun 2020 01:49:06: Fewer paired peaks (618) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 618 pairs to build model! INFO @ Tue, 30 Jun 2020 01:49:06: start model_add_line... INFO @ Tue, 30 Jun 2020 01:49:06: start X-correlation... INFO @ Tue, 30 Jun 2020 01:49:06: end of X-cor INFO @ Tue, 30 Jun 2020 01:49:06: #2 finished! INFO @ Tue, 30 Jun 2020 01:49:06: #2 predicted fragment length is 89 bps INFO @ Tue, 30 Jun 2020 01:49:06: #2 alternative fragment length(s) may be 4,89 bps INFO @ Tue, 30 Jun 2020 01:49:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX209932/SRX209932.20_model.r INFO @ Tue, 30 Jun 2020 01:49:06: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:49:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:49:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX209932/SRX209932.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:49:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX209932/SRX209932.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:49:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX209932/SRX209932.10_summits.bed INFO @ Tue, 30 Jun 2020 01:49:07: Done! pass1 - making usageList (459 chroms): 1 millis pass2 - checking and writing primary data (1752 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:49:26: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:49:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX209932/SRX209932.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:49:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX209932/SRX209932.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:49:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX209932/SRX209932.20_summits.bed INFO @ Tue, 30 Jun 2020 01:49:37: Done! pass1 - making usageList (329 chroms): 1 millis pass2 - checking and writing primary data (822 records, 4 fields): 12 millis CompletedMACS2peakCalling