Job ID = 6459869 SRX = SRX914964 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:45:49 prefetch.2.10.7: 1) Downloading 'SRR1873274'... 2020-06-21T13:45:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:46:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:46:58 prefetch.2.10.7: 'SRR1873274' is valid 2020-06-21T13:46:58 prefetch.2.10.7: 1) 'SRR1873274' was downloaded successfully Read 8519226 spots for SRR1873274/SRR1873274.sra Written 8519226 spots for SRR1873274/SRR1873274.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: 00:01:17 8519226 reads; of these: 8519226 (100.00%) were unpaired; of these: 5197274 (61.01%) aligned 0 times 2833572 (33.26%) aligned exactly 1 time 488380 (5.73%) aligned >1 times 38.99% overall alignment rate Time searching: 00:01:17 Overall time: 00:01:17 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] 2387865 / 3321952 = 0.7188 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 22:49:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX914964/SRX914964.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX914964/SRX914964.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX914964/SRX914964.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX914964/SRX914964.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 22:49:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:49:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:49:57: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:49:57: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:49:57: #1 total tags in treatment: 934087 INFO @ Sun, 21 Jun 2020 22:49:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:49:57: #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 22:49:57: #1 tags after filtering in treatment: 933565 INFO @ Sun, 21 Jun 2020 22:49:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:49:57: #1 finished! INFO @ Sun, 21 Jun 2020 22:49:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:49:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:49:57: #2 number of paired peaks: 984 WARNING @ Sun, 21 Jun 2020 22:49:57: Fewer paired peaks (984) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 984 pairs to build model! INFO @ Sun, 21 Jun 2020 22:49:57: start model_add_line... INFO @ Sun, 21 Jun 2020 22:49:57: start X-correlation... INFO @ Sun, 21 Jun 2020 22:49:57: end of X-cor INFO @ Sun, 21 Jun 2020 22:49:57: #2 finished! INFO @ Sun, 21 Jun 2020 22:49:57: #2 predicted fragment length is 150 bps INFO @ Sun, 21 Jun 2020 22:49:57: #2 alternative fragment length(s) may be 150,180,587 bps INFO @ Sun, 21 Jun 2020 22:49:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX914964/SRX914964.05_model.r INFO @ Sun, 21 Jun 2020 22:49:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:49:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:50:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:50:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX914964/SRX914964.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:50:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX914964/SRX914964.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:50:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX914964/SRX914964.05_summits.bed INFO @ Sun, 21 Jun 2020 22:50:01: Done! pass1 - making usageList (82 chroms): 1 millis pass2 - checking and writing primary data (205 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 22:50:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX914964/SRX914964.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX914964/SRX914964.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX914964/SRX914964.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX914964/SRX914964.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 22:50:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:50:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:50:27: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:50:27: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:50:27: #1 total tags in treatment: 934087 INFO @ Sun, 21 Jun 2020 22:50:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:50:27: #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 22:50:27: #1 tags after filtering in treatment: 933565 INFO @ Sun, 21 Jun 2020 22:50:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:50:27: #1 finished! INFO @ Sun, 21 Jun 2020 22:50:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:50:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:50:27: #2 number of paired peaks: 984 WARNING @ Sun, 21 Jun 2020 22:50:27: Fewer paired peaks (984) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 984 pairs to build model! INFO @ Sun, 21 Jun 2020 22:50:27: start model_add_line... INFO @ Sun, 21 Jun 2020 22:50:27: start X-correlation... INFO @ Sun, 21 Jun 2020 22:50:27: end of X-cor INFO @ Sun, 21 Jun 2020 22:50:27: #2 finished! INFO @ Sun, 21 Jun 2020 22:50:27: #2 predicted fragment length is 150 bps INFO @ Sun, 21 Jun 2020 22:50:27: #2 alternative fragment length(s) may be 150,180,587 bps INFO @ Sun, 21 Jun 2020 22:50:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX914964/SRX914964.10_model.r INFO @ Sun, 21 Jun 2020 22:50:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:50:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:50:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:50:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX914964/SRX914964.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:50:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX914964/SRX914964.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:50:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX914964/SRX914964.10_summits.bed INFO @ Sun, 21 Jun 2020 22:50:31: Done! pass1 - making usageList (64 chroms): 1 millis pass2 - checking and writing primary data (103 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 22:50:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX914964/SRX914964.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX914964/SRX914964.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX914964/SRX914964.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX914964/SRX914964.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 22:50:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:50:50: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:50:56: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:50:56: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:50:56: #1 total tags in treatment: 934087 INFO @ Sun, 21 Jun 2020 22:50:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:50:56: #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 22:50:56: #1 tags after filtering in treatment: 933565 INFO @ Sun, 21 Jun 2020 22:50:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:50:56: #1 finished! INFO @ Sun, 21 Jun 2020 22:50:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:50:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:50:57: #2 number of paired peaks: 984 WARNING @ Sun, 21 Jun 2020 22:50:57: Fewer paired peaks (984) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 984 pairs to build model! INFO @ Sun, 21 Jun 2020 22:50:57: start model_add_line... INFO @ Sun, 21 Jun 2020 22:50:57: start X-correlation... INFO @ Sun, 21 Jun 2020 22:50:57: end of X-cor INFO @ Sun, 21 Jun 2020 22:50:57: #2 finished! INFO @ Sun, 21 Jun 2020 22:50:57: #2 predicted fragment length is 150 bps INFO @ Sun, 21 Jun 2020 22:50:57: #2 alternative fragment length(s) may be 150,180,587 bps INFO @ Sun, 21 Jun 2020 22:50:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX914964/SRX914964.20_model.r INFO @ Sun, 21 Jun 2020 22:50:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:50:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:50:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:51:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX914964/SRX914964.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:51:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX914964/SRX914964.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:51:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX914964/SRX914964.20_summits.bed INFO @ Sun, 21 Jun 2020 22:51:01: Done! pass1 - making usageList (18 chroms): 2 millis pass2 - checking and writing primary data (21 records, 4 fields): 1 millis CompletedMACS2peakCalling