Job ID = 6456480 SRX = SRX348465 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:52:16 prefetch.2.10.7: 1) Downloading 'SRR976149'... 2020-06-21T10:52:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:53:28 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:53:29 prefetch.2.10.7: 'SRR976149' is valid 2020-06-21T10:53:29 prefetch.2.10.7: 1) 'SRR976149' was downloaded successfully Read 10528585 spots for SRR976149/SRR976149.sra Written 10528585 spots for SRR976149/SRR976149.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: 00:02:04 10528585 reads; of these: 10528585 (100.00%) were unpaired; of these: 1647551 (15.65%) aligned 0 times 6623869 (62.91%) aligned exactly 1 time 2257165 (21.44%) aligned >1 times 84.35% overall alignment rate Time searching: 00:02:04 Overall time: 00:02:04 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] 1794694 / 8881034 = 0.2021 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 19:58:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX348465/SRX348465.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX348465/SRX348465.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX348465/SRX348465.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX348465/SRX348465.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 19:58:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:58:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:58:40: 1000000 INFO @ Sun, 21 Jun 2020 19:58:47: 2000000 INFO @ Sun, 21 Jun 2020 19:58:53: 3000000 INFO @ Sun, 21 Jun 2020 19:59:00: 4000000 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 19:59:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX348465/SRX348465.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX348465/SRX348465.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX348465/SRX348465.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX348465/SRX348465.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 19:59:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:59:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:59:07: 5000000 INFO @ Sun, 21 Jun 2020 19:59:11: 1000000 INFO @ Sun, 21 Jun 2020 19:59:15: 6000000 INFO @ Sun, 21 Jun 2020 19:59:19: 2000000 INFO @ Sun, 21 Jun 2020 19:59:22: 7000000 INFO @ Sun, 21 Jun 2020 19:59:23: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 19:59:23: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 19:59:23: #1 total tags in treatment: 7086340 INFO @ Sun, 21 Jun 2020 19:59:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:59:23: #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 19:59:23: #1 tags after filtering in treatment: 7086328 INFO @ Sun, 21 Jun 2020 19:59:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:59:23: #1 finished! INFO @ Sun, 21 Jun 2020 19:59:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:59:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:59:24: #2 number of paired peaks: 932 WARNING @ Sun, 21 Jun 2020 19:59:24: Fewer paired peaks (932) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 932 pairs to build model! INFO @ Sun, 21 Jun 2020 19:59:24: start model_add_line... INFO @ Sun, 21 Jun 2020 19:59:24: start X-correlation... INFO @ Sun, 21 Jun 2020 19:59:24: end of X-cor INFO @ Sun, 21 Jun 2020 19:59:24: #2 finished! INFO @ Sun, 21 Jun 2020 19:59:24: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 19:59:24: #2 alternative fragment length(s) may be 91 bps INFO @ Sun, 21 Jun 2020 19:59:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX348465/SRX348465.05_model.r INFO @ Sun, 21 Jun 2020 19:59:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:59:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:59:26: 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 19:59:33: 4000000 INFO @ Sun, 21 Jun 2020 19:59:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX348465/SRX348465.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX348465/SRX348465.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX348465/SRX348465.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX348465/SRX348465.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 19:59:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:59:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:59:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:59:40: 5000000 INFO @ Sun, 21 Jun 2020 19:59:41: 1000000 INFO @ Sun, 21 Jun 2020 19:59:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX348465/SRX348465.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:59:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX348465/SRX348465.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:59:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX348465/SRX348465.05_summits.bed INFO @ Sun, 21 Jun 2020 19:59:47: Done! pass1 - making usageList (594 chroms): 2 millis pass2 - checking and writing primary data (4090 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:59:48: 6000000 INFO @ Sun, 21 Jun 2020 19:59:48: 2000000 INFO @ Sun, 21 Jun 2020 19:59:55: 7000000 INFO @ Sun, 21 Jun 2020 19:59:56: 3000000 INFO @ Sun, 21 Jun 2020 19:59:56: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 19:59:56: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 19:59:56: #1 total tags in treatment: 7086340 INFO @ Sun, 21 Jun 2020 19:59:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:59:56: #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 19:59:56: #1 tags after filtering in treatment: 7086328 INFO @ Sun, 21 Jun 2020 19:59:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:59:56: #1 finished! INFO @ Sun, 21 Jun 2020 19:59:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:59:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:59:57: #2 number of paired peaks: 932 WARNING @ Sun, 21 Jun 2020 19:59:57: Fewer paired peaks (932) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 932 pairs to build model! INFO @ Sun, 21 Jun 2020 19:59:57: start model_add_line... INFO @ Sun, 21 Jun 2020 19:59:57: start X-correlation... INFO @ Sun, 21 Jun 2020 19:59:57: end of X-cor INFO @ Sun, 21 Jun 2020 19:59:57: #2 finished! INFO @ Sun, 21 Jun 2020 19:59:57: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 19:59:57: #2 alternative fragment length(s) may be 91 bps INFO @ Sun, 21 Jun 2020 19:59:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX348465/SRX348465.10_model.r INFO @ Sun, 21 Jun 2020 19:59:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:59:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:00:02: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:00:09: 5000000 INFO @ Sun, 21 Jun 2020 20:00:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:00:16: 6000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:00:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX348465/SRX348465.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:00:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX348465/SRX348465.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:00:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX348465/SRX348465.10_summits.bed INFO @ Sun, 21 Jun 2020 20:00:21: Done! pass1 - making usageList (494 chroms): 1 millis pass2 - checking and writing primary data (2470 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:00:23: 7000000 INFO @ Sun, 21 Jun 2020 20:00:23: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 20:00:23: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 20:00:23: #1 total tags in treatment: 7086340 INFO @ Sun, 21 Jun 2020 20:00:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:00:23: #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 20:00:24: #1 tags after filtering in treatment: 7086328 INFO @ Sun, 21 Jun 2020 20:00:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:00:24: #1 finished! INFO @ Sun, 21 Jun 2020 20:00:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:00:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:00:24: #2 number of paired peaks: 932 WARNING @ Sun, 21 Jun 2020 20:00:24: Fewer paired peaks (932) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 932 pairs to build model! INFO @ Sun, 21 Jun 2020 20:00:24: start model_add_line... INFO @ Sun, 21 Jun 2020 20:00:24: start X-correlation... INFO @ Sun, 21 Jun 2020 20:00:24: end of X-cor INFO @ Sun, 21 Jun 2020 20:00:24: #2 finished! INFO @ Sun, 21 Jun 2020 20:00:24: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 20:00:24: #2 alternative fragment length(s) may be 91 bps INFO @ Sun, 21 Jun 2020 20:00:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX348465/SRX348465.20_model.r INFO @ Sun, 21 Jun 2020 20:00:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:00:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:00:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:00:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX348465/SRX348465.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:00:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX348465/SRX348465.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:00:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX348465/SRX348465.20_summits.bed INFO @ Sun, 21 Jun 2020 20:00:47: Done! pass1 - making usageList (169 chroms): 1 millis pass2 - checking and writing primary data (908 records, 4 fields): 6 millis CompletedMACS2peakCalling