Job ID = 6452415 SRX = SRX013044 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:31:27 prefetch.2.10.7: 1) Downloading 'SRR030310'... 2020-06-21T07:31:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:32:19 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:32:20 prefetch.2.10.7: 'SRR030310' is valid 2020-06-21T07:32:20 prefetch.2.10.7: 1) 'SRR030310' was downloaded successfully Read 5034276 spots for SRR030310/SRR030310.sra Written 5034276 spots for SRR030310/SRR030310.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: 00:00:54 5034276 reads; of these: 5034276 (100.00%) were unpaired; of these: 481100 (9.56%) aligned 0 times 3911244 (77.69%) aligned exactly 1 time 641932 (12.75%) aligned >1 times 90.44% overall alignment rate Time searching: 00:00:54 Overall time: 00:00:54 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] 229914 / 4553176 = 0.0505 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 16:35:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013044/SRX013044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013044/SRX013044.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013044/SRX013044.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013044/SRX013044.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 16:35:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:35:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:35:09: 1000000 INFO @ Sun, 21 Jun 2020 16:35:15: 2000000 INFO @ Sun, 21 Jun 2020 16:35:20: 3000000 INFO @ Sun, 21 Jun 2020 16:35:27: 4000000 INFO @ Sun, 21 Jun 2020 16:35:29: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:35:29: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:35:29: #1 total tags in treatment: 4323262 INFO @ Sun, 21 Jun 2020 16:35:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:35:29: #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 16:35:29: #1 tags after filtering in treatment: 4323151 INFO @ Sun, 21 Jun 2020 16:35:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:35:29: #1 finished! INFO @ Sun, 21 Jun 2020 16:35:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:35:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:35:29: #2 number of paired peaks: 254 WARNING @ Sun, 21 Jun 2020 16:35:29: Fewer paired peaks (254) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 254 pairs to build model! INFO @ Sun, 21 Jun 2020 16:35:29: start model_add_line... INFO @ Sun, 21 Jun 2020 16:35:29: start X-correlation... INFO @ Sun, 21 Jun 2020 16:35:29: end of X-cor INFO @ Sun, 21 Jun 2020 16:35:29: #2 finished! INFO @ Sun, 21 Jun 2020 16:35:29: #2 predicted fragment length is 134 bps INFO @ Sun, 21 Jun 2020 16:35:29: #2 alternative fragment length(s) may be 134,576 bps INFO @ Sun, 21 Jun 2020 16:35:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013044/SRX013044.05_model.r INFO @ Sun, 21 Jun 2020 16:35:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:35:29: #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 @ Sun, 21 Jun 2020 16:35:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013044/SRX013044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013044/SRX013044.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013044/SRX013044.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013044/SRX013044.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 16:35:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:35:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:35:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:35:40: 1000000 INFO @ Sun, 21 Jun 2020 16:35:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013044/SRX013044.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:35:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013044/SRX013044.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:35:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013044/SRX013044.05_summits.bed INFO @ Sun, 21 Jun 2020 16:35:45: Done! pass1 - making usageList (112 chroms): 1 millis pass2 - checking and writing primary data (1371 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:35:47: 2000000 INFO @ Sun, 21 Jun 2020 16:35:54: 3000000 INFO @ Sun, 21 Jun 2020 16:36:01: 4000000 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 16:36:03: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:36:03: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:36:03: #1 total tags in treatment: 4323262 INFO @ Sun, 21 Jun 2020 16:36:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:36:03: #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 16:36:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013044/SRX013044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013044/SRX013044.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013044/SRX013044.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013044/SRX013044.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 16:36:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:36:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:36:04: #1 tags after filtering in treatment: 4323151 INFO @ Sun, 21 Jun 2020 16:36:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:36:04: #1 finished! INFO @ Sun, 21 Jun 2020 16:36:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:36:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:36:04: #2 number of paired peaks: 254 WARNING @ Sun, 21 Jun 2020 16:36:04: Fewer paired peaks (254) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 254 pairs to build model! INFO @ Sun, 21 Jun 2020 16:36:04: start model_add_line... INFO @ Sun, 21 Jun 2020 16:36:04: start X-correlation... INFO @ Sun, 21 Jun 2020 16:36:04: end of X-cor INFO @ Sun, 21 Jun 2020 16:36:04: #2 finished! INFO @ Sun, 21 Jun 2020 16:36:04: #2 predicted fragment length is 134 bps INFO @ Sun, 21 Jun 2020 16:36:04: #2 alternative fragment length(s) may be 134,576 bps INFO @ Sun, 21 Jun 2020 16:36:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013044/SRX013044.10_model.r INFO @ Sun, 21 Jun 2020 16:36:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:36:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:36:09: 1000000 INFO @ Sun, 21 Jun 2020 16:36:15: 2000000 INFO @ Sun, 21 Jun 2020 16:36:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:36:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013044/SRX013044.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:36:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013044/SRX013044.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:36:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013044/SRX013044.10_summits.bed INFO @ Sun, 21 Jun 2020 16:36:20: Done! INFO @ Sun, 21 Jun 2020 16:36:20: 3000000 pass1 - making usageList (79 chroms): 1 millis pass2 - checking and writing primary data (358 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:36:26: 4000000 INFO @ Sun, 21 Jun 2020 16:36:28: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:36:28: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:36:28: #1 total tags in treatment: 4323262 INFO @ Sun, 21 Jun 2020 16:36:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:36:28: #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 16:36:29: #1 tags after filtering in treatment: 4323151 INFO @ Sun, 21 Jun 2020 16:36:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:36:29: #1 finished! INFO @ Sun, 21 Jun 2020 16:36:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:36:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:36:29: #2 number of paired peaks: 254 WARNING @ Sun, 21 Jun 2020 16:36:29: Fewer paired peaks (254) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 254 pairs to build model! INFO @ Sun, 21 Jun 2020 16:36:29: start model_add_line... INFO @ Sun, 21 Jun 2020 16:36:29: start X-correlation... INFO @ Sun, 21 Jun 2020 16:36:29: end of X-cor INFO @ Sun, 21 Jun 2020 16:36:29: #2 finished! INFO @ Sun, 21 Jun 2020 16:36:29: #2 predicted fragment length is 134 bps INFO @ Sun, 21 Jun 2020 16:36:29: #2 alternative fragment length(s) may be 134,576 bps INFO @ Sun, 21 Jun 2020 16:36:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013044/SRX013044.20_model.r INFO @ Sun, 21 Jun 2020 16:36:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:36:29: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:36:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:36:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013044/SRX013044.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:36:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013044/SRX013044.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:36:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013044/SRX013044.20_summits.bed INFO @ Sun, 21 Jun 2020 16:36:45: Done! pass1 - making usageList (52 chroms): 1 millis pass2 - checking and writing primary data (84 records, 4 fields): 4 millis CompletedMACS2peakCalling