Job ID = 6454855 SRX = SRX2592447 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:46:10 prefetch.2.10.7: 1) Downloading 'SRR5289724'... 2020-06-21T09:46:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:47:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:47:24 prefetch.2.10.7: 'SRR5289724' is valid 2020-06-21T09:47:24 prefetch.2.10.7: 1) 'SRR5289724' was downloaded successfully Read 7994586 spots for SRR5289724/SRR5289724.sra Written 7994586 spots for SRR5289724/SRR5289724.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: 00:01:54 7994586 reads; of these: 7994586 (100.00%) were unpaired; of these: 3943085 (49.32%) aligned 0 times 2955164 (36.96%) aligned exactly 1 time 1096337 (13.71%) aligned >1 times 50.68% overall alignment rate Time searching: 00:01:54 Overall time: 00:01:54 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] 2533953 / 4051501 = 0.6254 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 18:51:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592447/SRX2592447.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592447/SRX2592447.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592447/SRX2592447.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592447/SRX2592447.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 18:51:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:51:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:51:12: 1000000 INFO @ Sun, 21 Jun 2020 18:51:15: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:51:15: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:51:15: #1 total tags in treatment: 1517548 INFO @ Sun, 21 Jun 2020 18:51:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:51:15: #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 18:51:16: #1 tags after filtering in treatment: 1517260 INFO @ Sun, 21 Jun 2020 18:51:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:51:16: #1 finished! INFO @ Sun, 21 Jun 2020 18:51:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:51:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:51:16: #2 number of paired peaks: 748 WARNING @ Sun, 21 Jun 2020 18:51:16: Fewer paired peaks (748) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 748 pairs to build model! INFO @ Sun, 21 Jun 2020 18:51:16: start model_add_line... INFO @ Sun, 21 Jun 2020 18:51:16: start X-correlation... INFO @ Sun, 21 Jun 2020 18:51:16: end of X-cor INFO @ Sun, 21 Jun 2020 18:51:16: #2 finished! INFO @ Sun, 21 Jun 2020 18:51:16: #2 predicted fragment length is 138 bps INFO @ Sun, 21 Jun 2020 18:51:16: #2 alternative fragment length(s) may be 84,138,173,193 bps INFO @ Sun, 21 Jun 2020 18:51:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592447/SRX2592447.05_model.r INFO @ Sun, 21 Jun 2020 18:51:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:51:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:51:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:51:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592447/SRX2592447.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:51:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592447/SRX2592447.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:51:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592447/SRX2592447.05_summits.bed INFO @ Sun, 21 Jun 2020 18:51:22: Done! pass1 - making usageList (254 chroms): 2 millis pass2 - checking and writing primary data (7406 records, 4 fields): 14 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 18:51:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592447/SRX2592447.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592447/SRX2592447.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592447/SRX2592447.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592447/SRX2592447.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 18:51:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:51:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:51:42: 1000000 INFO @ Sun, 21 Jun 2020 18:51:46: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:51:46: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:51:46: #1 total tags in treatment: 1517548 INFO @ Sun, 21 Jun 2020 18:51:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:51:46: #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 18:51:46: #1 tags after filtering in treatment: 1517260 INFO @ Sun, 21 Jun 2020 18:51:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:51:46: #1 finished! INFO @ Sun, 21 Jun 2020 18:51:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:51:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:51:47: #2 number of paired peaks: 748 WARNING @ Sun, 21 Jun 2020 18:51:47: Fewer paired peaks (748) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 748 pairs to build model! INFO @ Sun, 21 Jun 2020 18:51:47: start model_add_line... INFO @ Sun, 21 Jun 2020 18:51:47: start X-correlation... INFO @ Sun, 21 Jun 2020 18:51:47: end of X-cor INFO @ Sun, 21 Jun 2020 18:51:47: #2 finished! INFO @ Sun, 21 Jun 2020 18:51:47: #2 predicted fragment length is 138 bps INFO @ Sun, 21 Jun 2020 18:51:47: #2 alternative fragment length(s) may be 84,138,173,193 bps INFO @ Sun, 21 Jun 2020 18:51:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592447/SRX2592447.10_model.r INFO @ Sun, 21 Jun 2020 18:51:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:51:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:51:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:51:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592447/SRX2592447.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:51:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592447/SRX2592447.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:51:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592447/SRX2592447.10_summits.bed INFO @ Sun, 21 Jun 2020 18:51:53: Done! pass1 - making usageList (162 chroms): 1 millis pass2 - checking and writing primary data (3316 records, 4 fields): 9 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 18:52:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592447/SRX2592447.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592447/SRX2592447.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592447/SRX2592447.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592447/SRX2592447.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 18:52:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:52:05: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:52:12: 1000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:52:16: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:52:16: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:52:16: #1 total tags in treatment: 1517548 INFO @ Sun, 21 Jun 2020 18:52:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:52:16: #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 18:52:16: #1 tags after filtering in treatment: 1517260 INFO @ Sun, 21 Jun 2020 18:52:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:52:16: #1 finished! INFO @ Sun, 21 Jun 2020 18:52:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:52:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:52:16: #2 number of paired peaks: 748 WARNING @ Sun, 21 Jun 2020 18:52:16: Fewer paired peaks (748) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 748 pairs to build model! INFO @ Sun, 21 Jun 2020 18:52:16: start model_add_line... INFO @ Sun, 21 Jun 2020 18:52:16: start X-correlation... INFO @ Sun, 21 Jun 2020 18:52:16: end of X-cor INFO @ Sun, 21 Jun 2020 18:52:16: #2 finished! INFO @ Sun, 21 Jun 2020 18:52:16: #2 predicted fragment length is 138 bps INFO @ Sun, 21 Jun 2020 18:52:16: #2 alternative fragment length(s) may be 84,138,173,193 bps INFO @ Sun, 21 Jun 2020 18:52:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592447/SRX2592447.20_model.r INFO @ Sun, 21 Jun 2020 18:52:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:52:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:52:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:52:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592447/SRX2592447.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:52:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592447/SRX2592447.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:52:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592447/SRX2592447.20_summits.bed INFO @ Sun, 21 Jun 2020 18:52:23: Done! pass1 - making usageList (95 chroms): 1 millis pass2 - checking and writing primary data (766 records, 4 fields): 6 millis CompletedMACS2peakCalling