Job ID = 6454842 SRX = SRX2592437 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:46:55 prefetch.2.10.7: 1) Downloading 'SRR5289714'... 2020-06-21T09:46:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:48:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:48:49 prefetch.2.10.7: 'SRR5289714' is valid 2020-06-21T09:48:49 prefetch.2.10.7: 1) 'SRR5289714' was downloaded successfully Read 10095293 spots for SRR5289714/SRR5289714.sra Written 10095293 spots for SRR5289714/SRR5289714.sra 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 10095293 reads; of these: 10095293 (100.00%) were unpaired; of these: 955433 (9.46%) aligned 0 times 8162032 (80.85%) aligned exactly 1 time 977828 (9.69%) aligned >1 times 90.54% 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] 4812935 / 9139860 = 0.5266 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 @ Sun, 21 Jun 2020 18:54:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592437/SRX2592437.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592437/SRX2592437.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592437/SRX2592437.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592437/SRX2592437.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 @ Sun, 21 Jun 2020 18:54:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:54:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:54:41: 1000000 INFO @ Sun, 21 Jun 2020 18:54:48: 2000000 INFO @ Sun, 21 Jun 2020 18:54:54: 3000000 INFO @ Sun, 21 Jun 2020 18:55:01: 4000000 INFO @ Sun, 21 Jun 2020 18:55:03: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:55:03: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:55:03: #1 total tags in treatment: 4326925 INFO @ Sun, 21 Jun 2020 18:55:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:55:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 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 @ Sun, 21 Jun 2020 18:55:03: #1 tags after filtering in treatment: 4326387 INFO @ Sun, 21 Jun 2020 18:55:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:55:03: #1 finished! INFO @ Sun, 21 Jun 2020 18:55:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:55:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:55:04: #2 number of paired peaks: 330 WARNING @ Sun, 21 Jun 2020 18:55:04: Fewer paired peaks (330) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 330 pairs to build model! INFO @ Sun, 21 Jun 2020 18:55:04: start model_add_line... INFO @ Sun, 21 Jun 2020 18:55:04: start X-correlation... INFO @ Sun, 21 Jun 2020 18:55:04: end of X-cor INFO @ Sun, 21 Jun 2020 18:55:04: #2 finished! INFO @ Sun, 21 Jun 2020 18:55:04: #2 predicted fragment length is 217 bps INFO @ Sun, 21 Jun 2020 18:55:04: #2 alternative fragment length(s) may be 217 bps INFO @ Sun, 21 Jun 2020 18:55:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592437/SRX2592437.05_model.r INFO @ Sun, 21 Jun 2020 18:55:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:55:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:55:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592437/SRX2592437.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592437/SRX2592437.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592437/SRX2592437.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592437/SRX2592437.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 @ Sun, 21 Jun 2020 18:55:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:55:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:55:13: 1000000 INFO @ Sun, 21 Jun 2020 18:55:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:55:20: 2000000 INFO @ Sun, 21 Jun 2020 18:55:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592437/SRX2592437.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:55:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592437/SRX2592437.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:55:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592437/SRX2592437.05_summits.bed INFO @ Sun, 21 Jun 2020 18:55:25: Done! pass1 - making usageList (206 chroms): 3 millis pass2 - checking and writing primary data (14689 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:55:28: 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 @ Sun, 21 Jun 2020 18:55:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592437/SRX2592437.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592437/SRX2592437.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592437/SRX2592437.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592437/SRX2592437.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 @ Sun, 21 Jun 2020 18:55:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:55:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:55:36: 4000000 INFO @ Sun, 21 Jun 2020 18:55:39: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:55:39: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:55:39: #1 total tags in treatment: 4326925 INFO @ Sun, 21 Jun 2020 18:55:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:55:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:55:39: #1 tags after filtering in treatment: 4326387 INFO @ Sun, 21 Jun 2020 18:55:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:55:39: #1 finished! INFO @ Sun, 21 Jun 2020 18:55:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:55:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:55:40: #2 number of paired peaks: 330 WARNING @ Sun, 21 Jun 2020 18:55:40: Fewer paired peaks (330) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 330 pairs to build model! INFO @ Sun, 21 Jun 2020 18:55:40: start model_add_line... INFO @ Sun, 21 Jun 2020 18:55:40: start X-correlation... INFO @ Sun, 21 Jun 2020 18:55:40: end of X-cor INFO @ Sun, 21 Jun 2020 18:55:40: #2 finished! INFO @ Sun, 21 Jun 2020 18:55:40: #2 predicted fragment length is 217 bps INFO @ Sun, 21 Jun 2020 18:55:40: #2 alternative fragment length(s) may be 217 bps INFO @ Sun, 21 Jun 2020 18:55:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592437/SRX2592437.10_model.r INFO @ Sun, 21 Jun 2020 18:55:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:55:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:55:42: 1000000 INFO @ Sun, 21 Jun 2020 18:55:49: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:55:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:55:56: 3000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:56:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592437/SRX2592437.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:56:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592437/SRX2592437.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:56:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592437/SRX2592437.10_summits.bed INFO @ Sun, 21 Jun 2020 18:56:00: Done! INFO @ Sun, 21 Jun 2020 18:56:02: 4000000 INFO @ Sun, 21 Jun 2020 18:56:04: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:56:04: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:56:04: #1 total tags in treatment: 4326925 INFO @ Sun, 21 Jun 2020 18:56:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:56:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:56:05: #1 tags after filtering in treatment: 4326387 INFO @ Sun, 21 Jun 2020 18:56:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:56:05: #1 finished! INFO @ Sun, 21 Jun 2020 18:56:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:56:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:56:06: #2 number of paired peaks: 330 WARNING @ Sun, 21 Jun 2020 18:56:06: Fewer paired peaks (330) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 330 pairs to build model! INFO @ Sun, 21 Jun 2020 18:56:06: start model_add_line... INFO @ Sun, 21 Jun 2020 18:56:06: start X-correlation... INFO @ Sun, 21 Jun 2020 18:56:06: end of X-cor INFO @ Sun, 21 Jun 2020 18:56:06: #2 finished! INFO @ Sun, 21 Jun 2020 18:56:06: #2 predicted fragment length is 217 bps INFO @ Sun, 21 Jun 2020 18:56:06: #2 alternative fragment length(s) may be 217 bps INFO @ Sun, 21 Jun 2020 18:56:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592437/SRX2592437.20_model.r INFO @ Sun, 21 Jun 2020 18:56:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:56:06: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (158 chroms): 3 millis pass2 - checking and writing primary data (12643 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:56:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:56:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592437/SRX2592437.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:56:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592437/SRX2592437.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:56:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592437/SRX2592437.20_summits.bed INFO @ Sun, 21 Jun 2020 18:56:25: Done! pass1 - making usageList (100 chroms): 3 millis pass2 - checking and writing primary data (9932 records, 4 fields): 15 millis CompletedMACS2peakCalling