Job ID = 6452428 SRX = SRX013051 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:26:02 prefetch.2.10.7: 1) Downloading 'SRR030317'... 2020-06-21T07:26:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:26:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:26:43 prefetch.2.10.7: 'SRR030317' is valid 2020-06-21T07:26:43 prefetch.2.10.7: 1) 'SRR030317' was downloaded successfully Read 2867833 spots for SRR030317/SRR030317.sra Written 2867833 spots for SRR030317/SRR030317.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: 00:00:27 2867833 reads; of these: 2867833 (100.00%) were unpaired; of these: 759461 (26.48%) aligned 0 times 1821314 (63.51%) aligned exactly 1 time 287058 (10.01%) aligned >1 times 73.52% overall alignment rate Time searching: 00:00:27 Overall time: 00:00:27 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] 660470 / 2108372 = 0.3133 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 16:28:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013051/SRX013051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013051/SRX013051.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013051/SRX013051.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013051/SRX013051.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 16:28:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:28:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:28:18: 1000000 INFO @ Sun, 21 Jun 2020 16:28:20: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:28:20: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:28:20: #1 total tags in treatment: 1447902 INFO @ Sun, 21 Jun 2020 16:28:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:28:20: #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 16:28:20: #1 tags after filtering in treatment: 1447497 INFO @ Sun, 21 Jun 2020 16:28:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:28:20: #1 finished! INFO @ Sun, 21 Jun 2020 16:28:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:28:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:28:21: #2 number of paired peaks: 702 WARNING @ Sun, 21 Jun 2020 16:28:21: Fewer paired peaks (702) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 702 pairs to build model! INFO @ Sun, 21 Jun 2020 16:28:21: start model_add_line... INFO @ Sun, 21 Jun 2020 16:28:21: start X-correlation... INFO @ Sun, 21 Jun 2020 16:28:21: end of X-cor INFO @ Sun, 21 Jun 2020 16:28:21: #2 finished! INFO @ Sun, 21 Jun 2020 16:28:21: #2 predicted fragment length is 137 bps INFO @ Sun, 21 Jun 2020 16:28:21: #2 alternative fragment length(s) may be 137,566 bps INFO @ Sun, 21 Jun 2020 16:28:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013051/SRX013051.05_model.r INFO @ Sun, 21 Jun 2020 16:28:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:28:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:28:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:28:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013051/SRX013051.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:28:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013051/SRX013051.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:28:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013051/SRX013051.05_summits.bed INFO @ Sun, 21 Jun 2020 16:28:26: Done! pass1 - making usageList (58 chroms): 1 millis pass2 - checking and writing primary data (499 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 16:28:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013051/SRX013051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013051/SRX013051.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013051/SRX013051.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013051/SRX013051.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 16:28:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:28:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:28:48: 1000000 INFO @ Sun, 21 Jun 2020 16:28:51: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:28:51: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:28:51: #1 total tags in treatment: 1447902 INFO @ Sun, 21 Jun 2020 16:28:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:28:51: #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 16:28:51: #1 tags after filtering in treatment: 1447497 INFO @ Sun, 21 Jun 2020 16:28:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:28:51: #1 finished! INFO @ Sun, 21 Jun 2020 16:28:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:28:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:28:51: #2 number of paired peaks: 702 WARNING @ Sun, 21 Jun 2020 16:28:51: Fewer paired peaks (702) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 702 pairs to build model! INFO @ Sun, 21 Jun 2020 16:28:51: start model_add_line... INFO @ Sun, 21 Jun 2020 16:28:51: start X-correlation... INFO @ Sun, 21 Jun 2020 16:28:51: end of X-cor INFO @ Sun, 21 Jun 2020 16:28:51: #2 finished! INFO @ Sun, 21 Jun 2020 16:28:51: #2 predicted fragment length is 137 bps INFO @ Sun, 21 Jun 2020 16:28:51: #2 alternative fragment length(s) may be 137,566 bps INFO @ Sun, 21 Jun 2020 16:28:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013051/SRX013051.10_model.r INFO @ Sun, 21 Jun 2020 16:28:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:28:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:28:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:28:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013051/SRX013051.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:28:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013051/SRX013051.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:28:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013051/SRX013051.10_summits.bed INFO @ Sun, 21 Jun 2020 16:28:56: Done! pass1 - making usageList (45 chroms): 1 millis pass2 - checking and writing primary data (141 records, 4 fields): 4 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 16:29:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013051/SRX013051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013051/SRX013051.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013051/SRX013051.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013051/SRX013051.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 16:29:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:29:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:29:18: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:29:21: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:29:21: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:29:21: #1 total tags in treatment: 1447902 INFO @ Sun, 21 Jun 2020 16:29:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:29:21: #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 16:29:21: #1 tags after filtering in treatment: 1447497 INFO @ Sun, 21 Jun 2020 16:29:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:29:21: #1 finished! INFO @ Sun, 21 Jun 2020 16:29:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:29:21: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:29:21: #2 number of paired peaks: 702 WARNING @ Sun, 21 Jun 2020 16:29:21: Fewer paired peaks (702) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 702 pairs to build model! INFO @ Sun, 21 Jun 2020 16:29:21: start model_add_line... INFO @ Sun, 21 Jun 2020 16:29:21: start X-correlation... INFO @ Sun, 21 Jun 2020 16:29:21: end of X-cor INFO @ Sun, 21 Jun 2020 16:29:21: #2 finished! INFO @ Sun, 21 Jun 2020 16:29:21: #2 predicted fragment length is 137 bps INFO @ Sun, 21 Jun 2020 16:29:21: #2 alternative fragment length(s) may be 137,566 bps INFO @ Sun, 21 Jun 2020 16:29:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013051/SRX013051.20_model.r INFO @ Sun, 21 Jun 2020 16:29:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:29:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:29:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:29:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013051/SRX013051.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:29:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013051/SRX013051.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:29:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013051/SRX013051.20_summits.bed INFO @ Sun, 21 Jun 2020 16:29:27: Done! pass1 - making usageList (34 chroms): 0 millis pass2 - checking and writing primary data (50 records, 4 fields): 2 millis CompletedMACS2peakCalling