Job ID = 6454272 SRX = SRX193629 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:09:39 prefetch.2.10.7: 1) Downloading 'SRR586007'... 2020-06-21T09:09:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:12:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:12:25 prefetch.2.10.7: 'SRR586007' is valid 2020-06-21T09:12:25 prefetch.2.10.7: 1) 'SRR586007' was downloaded successfully Read 10988242 spots for SRR586007/SRR586007.sra Written 10988242 spots for SRR586007/SRR586007.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: 00:02:29 10988242 reads; of these: 10988242 (100.00%) were unpaired; of these: 3645314 (33.17%) aligned 0 times 4256764 (38.74%) aligned exactly 1 time 3086164 (28.09%) aligned >1 times 66.83% overall alignment rate Time searching: 00:02:29 Overall time: 00:02:29 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] 2550642 / 7342928 = 0.3474 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 18:17:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193629/SRX193629.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193629/SRX193629.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193629/SRX193629.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193629/SRX193629.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 18:17:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:17:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:17:44: 1000000 INFO @ Sun, 21 Jun 2020 18:17:51: 2000000 INFO @ Sun, 21 Jun 2020 18:17:57: 3000000 INFO @ Sun, 21 Jun 2020 18:18:03: 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 18:18:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193629/SRX193629.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193629/SRX193629.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193629/SRX193629.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193629/SRX193629.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 18:18:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:18:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:18:08: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:18:08: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:18:08: #1 total tags in treatment: 4792286 INFO @ Sun, 21 Jun 2020 18:18:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:18:08: #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 18:18:09: #1 tags after filtering in treatment: 4792181 INFO @ Sun, 21 Jun 2020 18:18:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:18:09: #1 finished! INFO @ Sun, 21 Jun 2020 18:18:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:18:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:18:09: #2 number of paired peaks: 2209 INFO @ Sun, 21 Jun 2020 18:18:09: start model_add_line... INFO @ Sun, 21 Jun 2020 18:18:09: start X-correlation... INFO @ Sun, 21 Jun 2020 18:18:09: end of X-cor INFO @ Sun, 21 Jun 2020 18:18:09: #2 finished! INFO @ Sun, 21 Jun 2020 18:18:09: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 18:18:09: #2 alternative fragment length(s) may be 4,59 bps INFO @ Sun, 21 Jun 2020 18:18:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193629/SRX193629.05_model.r WARNING @ Sun, 21 Jun 2020 18:18:09: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:18:09: #2 You may need to consider one of the other alternative d(s): 4,59 WARNING @ Sun, 21 Jun 2020 18:18:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:18:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:18:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:18:14: 1000000 INFO @ Sun, 21 Jun 2020 18:18:19: 2000000 INFO @ Sun, 21 Jun 2020 18:18:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:18:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193629/SRX193629.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:18:25: 3000000 INFO @ Sun, 21 Jun 2020 18:18:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193629/SRX193629.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:18:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193629/SRX193629.05_summits.bed INFO @ Sun, 21 Jun 2020 18:18:25: Done! pass1 - making usageList (767 chroms): 2 millis pass2 - checking and writing primary data (3349 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:18:30: 4000000 INFO @ Sun, 21 Jun 2020 18:18:34: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:18:34: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:18:34: #1 total tags in treatment: 4792286 INFO @ Sun, 21 Jun 2020 18:18:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:18:34: #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 18:18:35: #1 tags after filtering in treatment: 4792181 INFO @ Sun, 21 Jun 2020 18:18:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:18:35: #1 finished! INFO @ Sun, 21 Jun 2020 18:18:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:18:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:18:35: #2 number of paired peaks: 2209 INFO @ Sun, 21 Jun 2020 18:18:35: start model_add_line... INFO @ Sun, 21 Jun 2020 18:18:35: start X-correlation... INFO @ Sun, 21 Jun 2020 18:18:35: end of X-cor INFO @ Sun, 21 Jun 2020 18:18:35: #2 finished! INFO @ Sun, 21 Jun 2020 18:18:35: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 18:18:35: #2 alternative fragment length(s) may be 4,59 bps INFO @ Sun, 21 Jun 2020 18:18:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193629/SRX193629.10_model.r WARNING @ Sun, 21 Jun 2020 18:18:35: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:18:35: #2 You may need to consider one of the other alternative d(s): 4,59 WARNING @ Sun, 21 Jun 2020 18:18:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:18:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:18:35: #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 18:18:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193629/SRX193629.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193629/SRX193629.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193629/SRX193629.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193629/SRX193629.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 18:18:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:18:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:18:43: 1000000 INFO @ Sun, 21 Jun 2020 18:18:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:18:49: 2000000 INFO @ Sun, 21 Jun 2020 18:18:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193629/SRX193629.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:18:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193629/SRX193629.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:18:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193629/SRX193629.10_summits.bed INFO @ Sun, 21 Jun 2020 18:18:52: Done! pass1 - making usageList (640 chroms): 1 millis pass2 - checking and writing primary data (2259 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:18:54: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:19:00: 4000000 INFO @ Sun, 21 Jun 2020 18:19:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:19:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:19:04: #1 total tags in treatment: 4792286 INFO @ Sun, 21 Jun 2020 18:19:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:19:04: #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 18:19:05: #1 tags after filtering in treatment: 4792181 INFO @ Sun, 21 Jun 2020 18:19:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:19:05: #1 finished! INFO @ Sun, 21 Jun 2020 18:19:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:19:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:19:05: #2 number of paired peaks: 2209 INFO @ Sun, 21 Jun 2020 18:19:05: start model_add_line... INFO @ Sun, 21 Jun 2020 18:19:05: start X-correlation... INFO @ Sun, 21 Jun 2020 18:19:05: end of X-cor INFO @ Sun, 21 Jun 2020 18:19:05: #2 finished! INFO @ Sun, 21 Jun 2020 18:19:05: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 18:19:05: #2 alternative fragment length(s) may be 4,59 bps INFO @ Sun, 21 Jun 2020 18:19:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193629/SRX193629.20_model.r WARNING @ Sun, 21 Jun 2020 18:19:05: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:19:05: #2 You may need to consider one of the other alternative d(s): 4,59 WARNING @ Sun, 21 Jun 2020 18:19:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:19:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:19:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:19:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:19:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193629/SRX193629.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:19:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193629/SRX193629.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:19:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193629/SRX193629.20_summits.bed INFO @ Sun, 21 Jun 2020 18:19:21: Done! pass1 - making usageList (473 chroms): 1 millis pass2 - checking and writing primary data (1123 records, 4 fields): 33 millis CompletedMACS2peakCalling