Job ID = 6454380 SRX = SRX202123 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:02:34 prefetch.2.10.7: 1) Downloading 'SRR610269'... 2020-06-21T09:02:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:03:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:03:32 prefetch.2.10.7: 'SRR610269' is valid 2020-06-21T09:03:32 prefetch.2.10.7: 1) 'SRR610269' was downloaded successfully Read 13503799 spots for SRR610269/SRR610269.sra Written 13503799 spots for SRR610269/SRR610269.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: 00:01:51 13503799 reads; of these: 13503799 (100.00%) were unpaired; of these: 6947656 (51.45%) aligned 0 times 5200756 (38.51%) aligned exactly 1 time 1355387 (10.04%) aligned >1 times 48.55% overall alignment rate Time searching: 00:01:51 Overall time: 00:01:51 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] 2631717 / 6556143 = 0.4014 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 18:07:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX202123/SRX202123.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX202123/SRX202123.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX202123/SRX202123.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX202123/SRX202123.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 18:07:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:07:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:07:48: 1000000 INFO @ Sun, 21 Jun 2020 18:07:53: 2000000 INFO @ Sun, 21 Jun 2020 18:07:58: 3000000 INFO @ Sun, 21 Jun 2020 18:08:03: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:08:03: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:08:03: #1 total tags in treatment: 3924426 INFO @ Sun, 21 Jun 2020 18:08:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:08:03: #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 18:08:04: #1 tags after filtering in treatment: 3924261 INFO @ Sun, 21 Jun 2020 18:08:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:08:04: #1 finished! INFO @ Sun, 21 Jun 2020 18:08:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:08:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:08:04: #2 number of paired peaks: 2167 INFO @ Sun, 21 Jun 2020 18:08:04: start model_add_line... INFO @ Sun, 21 Jun 2020 18:08:04: start X-correlation... INFO @ Sun, 21 Jun 2020 18:08:04: end of X-cor INFO @ Sun, 21 Jun 2020 18:08:04: #2 finished! INFO @ Sun, 21 Jun 2020 18:08:04: #2 predicted fragment length is 86 bps INFO @ Sun, 21 Jun 2020 18:08:04: #2 alternative fragment length(s) may be 86 bps INFO @ Sun, 21 Jun 2020 18:08:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX202123/SRX202123.05_model.r INFO @ Sun, 21 Jun 2020 18:08:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:08:04: #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 18:08:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX202123/SRX202123.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX202123/SRX202123.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX202123/SRX202123.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX202123/SRX202123.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 18:08:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:08:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:08:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:08:19: 1000000 INFO @ Sun, 21 Jun 2020 18:08:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX202123/SRX202123.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:08:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX202123/SRX202123.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:08:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX202123/SRX202123.05_summits.bed INFO @ Sun, 21 Jun 2020 18:08:19: Done! pass1 - making usageList (501 chroms): 2 millis pass2 - checking and writing primary data (5347 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:08:23: 2000000 INFO @ Sun, 21 Jun 2020 18:08:28: 3000000 INFO @ Sun, 21 Jun 2020 18:08:33: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:08:33: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:08:33: #1 total tags in treatment: 3924426 INFO @ Sun, 21 Jun 2020 18:08:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:08:33: #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 18:08:34: #1 tags after filtering in treatment: 3924261 INFO @ Sun, 21 Jun 2020 18:08:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:08:34: #1 finished! INFO @ Sun, 21 Jun 2020 18:08:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:08:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:08:34: #2 number of paired peaks: 2167 INFO @ Sun, 21 Jun 2020 18:08:34: start model_add_line... INFO @ Sun, 21 Jun 2020 18:08:34: start X-correlation... INFO @ Sun, 21 Jun 2020 18:08:34: end of X-cor INFO @ Sun, 21 Jun 2020 18:08:34: #2 finished! INFO @ Sun, 21 Jun 2020 18:08:34: #2 predicted fragment length is 86 bps INFO @ Sun, 21 Jun 2020 18:08:34: #2 alternative fragment length(s) may be 86 bps INFO @ Sun, 21 Jun 2020 18:08:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX202123/SRX202123.10_model.r INFO @ Sun, 21 Jun 2020 18:08:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:08:34: #3 Pre-compute pvalue-qvalue table... 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 18:08:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX202123/SRX202123.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX202123/SRX202123.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX202123/SRX202123.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX202123/SRX202123.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 18:08:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:08:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:08:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:08:49: 1000000 INFO @ Sun, 21 Jun 2020 18:08:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX202123/SRX202123.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:08:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX202123/SRX202123.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:08:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX202123/SRX202123.10_summits.bed INFO @ Sun, 21 Jun 2020 18:08:49: Done! pass1 - making usageList (353 chroms): 1 millis pass2 - checking and writing primary data (2270 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:08:54: 2000000 INFO @ Sun, 21 Jun 2020 18:08:59: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:09:04: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:09:04: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:09:04: #1 total tags in treatment: 3924426 INFO @ Sun, 21 Jun 2020 18:09:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:09:04: #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 18:09:04: #1 tags after filtering in treatment: 3924261 INFO @ Sun, 21 Jun 2020 18:09:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:09:04: #1 finished! INFO @ Sun, 21 Jun 2020 18:09:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:09:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:09:05: #2 number of paired peaks: 2167 INFO @ Sun, 21 Jun 2020 18:09:05: start model_add_line... INFO @ Sun, 21 Jun 2020 18:09:05: start X-correlation... INFO @ Sun, 21 Jun 2020 18:09:05: end of X-cor INFO @ Sun, 21 Jun 2020 18:09:05: #2 finished! INFO @ Sun, 21 Jun 2020 18:09:05: #2 predicted fragment length is 86 bps INFO @ Sun, 21 Jun 2020 18:09:05: #2 alternative fragment length(s) may be 86 bps INFO @ Sun, 21 Jun 2020 18:09:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX202123/SRX202123.20_model.r INFO @ Sun, 21 Jun 2020 18:09:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:09:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:09:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:09:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX202123/SRX202123.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:09:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX202123/SRX202123.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:09:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX202123/SRX202123.20_summits.bed INFO @ Sun, 21 Jun 2020 18:09:20: Done! pass1 - making usageList (115 chroms): 1 millis pass2 - checking and writing primary data (568 records, 4 fields): 5 millis CompletedMACS2peakCalling