Job ID = 6454888 SRX = SRX2592476 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:51:55 prefetch.2.10.7: 1) Downloading 'SRR5289753'... 2020-06-21T09:51:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:54:02 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:54:02 prefetch.2.10.7: 'SRR5289753' is valid 2020-06-21T09:54:02 prefetch.2.10.7: 1) 'SRR5289753' was downloaded successfully Read 7672022 spots for SRR5289753/SRR5289753.sra Written 7672022 spots for SRR5289753/SRR5289753.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: 00:02:05 7672022 reads; of these: 7672022 (100.00%) were unpaired; of these: 2024695 (26.39%) aligned 0 times 4037454 (52.63%) aligned exactly 1 time 1609873 (20.98%) aligned >1 times 73.61% overall alignment rate Time searching: 00:02:05 Overall time: 00:02:05 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] 1358324 / 5647327 = 0.2405 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 18:58:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592476/SRX2592476.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592476/SRX2592476.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592476/SRX2592476.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592476/SRX2592476.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 18:58:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:58:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:58:29: 1000000 INFO @ Sun, 21 Jun 2020 18:58:34: 2000000 INFO @ Sun, 21 Jun 2020 18:58:39: 3000000 INFO @ Sun, 21 Jun 2020 18:58:44: 4000000 INFO @ Sun, 21 Jun 2020 18:58:46: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:58:46: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:58:46: #1 total tags in treatment: 4289003 INFO @ Sun, 21 Jun 2020 18:58:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:58:46: #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 18:58:46: #1 tags after filtering in treatment: 4288822 INFO @ Sun, 21 Jun 2020 18:58:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:58:46: #1 finished! INFO @ Sun, 21 Jun 2020 18:58:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:58:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:58:46: #2 number of paired peaks: 1039 INFO @ Sun, 21 Jun 2020 18:58:46: start model_add_line... INFO @ Sun, 21 Jun 2020 18:58:46: start X-correlation... INFO @ Sun, 21 Jun 2020 18:58:46: end of X-cor INFO @ Sun, 21 Jun 2020 18:58:46: #2 finished! INFO @ Sun, 21 Jun 2020 18:58:46: #2 predicted fragment length is 88 bps INFO @ Sun, 21 Jun 2020 18:58:46: #2 alternative fragment length(s) may be 88,595 bps INFO @ Sun, 21 Jun 2020 18:58:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592476/SRX2592476.05_model.r WARNING @ Sun, 21 Jun 2020 18:58:46: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:58:46: #2 You may need to consider one of the other alternative d(s): 88,595 WARNING @ Sun, 21 Jun 2020 18:58:46: #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 18:58:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:58:46: #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 18:58:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592476/SRX2592476.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592476/SRX2592476.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592476/SRX2592476.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592476/SRX2592476.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 18:58:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:58:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:58:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:59:00: 1000000 INFO @ Sun, 21 Jun 2020 18:59:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592476/SRX2592476.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:59:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592476/SRX2592476.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:59:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592476/SRX2592476.05_summits.bed INFO @ Sun, 21 Jun 2020 18:59:01: Done! pass1 - making usageList (509 chroms): 1 millis pass2 - checking and writing primary data (1872 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:59:05: 2000000 INFO @ Sun, 21 Jun 2020 18:59:11: 3000000 INFO @ Sun, 21 Jun 2020 18:59:16: 4000000 INFO @ Sun, 21 Jun 2020 18:59:18: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:59:18: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:59:18: #1 total tags in treatment: 4289003 INFO @ Sun, 21 Jun 2020 18:59:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:59:18: #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 18:59:18: #1 tags after filtering in treatment: 4288822 INFO @ Sun, 21 Jun 2020 18:59:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:59:18: #1 finished! INFO @ Sun, 21 Jun 2020 18:59:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:59:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:59:19: #2 number of paired peaks: 1039 INFO @ Sun, 21 Jun 2020 18:59:19: start model_add_line... INFO @ Sun, 21 Jun 2020 18:59:19: start X-correlation... INFO @ Sun, 21 Jun 2020 18:59:19: end of X-cor INFO @ Sun, 21 Jun 2020 18:59:19: #2 finished! INFO @ Sun, 21 Jun 2020 18:59:19: #2 predicted fragment length is 88 bps INFO @ Sun, 21 Jun 2020 18:59:19: #2 alternative fragment length(s) may be 88,595 bps INFO @ Sun, 21 Jun 2020 18:59:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592476/SRX2592476.10_model.r WARNING @ Sun, 21 Jun 2020 18:59:19: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:59:19: #2 You may need to consider one of the other alternative d(s): 88,595 WARNING @ Sun, 21 Jun 2020 18:59:19: #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 18:59:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:59:19: #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 18:59:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592476/SRX2592476.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592476/SRX2592476.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592476/SRX2592476.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592476/SRX2592476.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 18:59:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:59:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:59:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:59:30: 1000000 INFO @ Sun, 21 Jun 2020 18:59:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592476/SRX2592476.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:59:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592476/SRX2592476.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:59:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592476/SRX2592476.10_summits.bed INFO @ Sun, 21 Jun 2020 18:59:33: Done! pass1 - making usageList (413 chroms): 1 millis pass2 - checking and writing primary data (1036 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:59:35: 2000000 INFO @ Sun, 21 Jun 2020 18:59:40: 3000000 INFO @ Sun, 21 Jun 2020 18:59:46: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:59:48: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:59:48: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:59:48: #1 total tags in treatment: 4289003 INFO @ Sun, 21 Jun 2020 18:59:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:59:48: #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 18:59:48: #1 tags after filtering in treatment: 4288822 INFO @ Sun, 21 Jun 2020 18:59:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:59:48: #1 finished! INFO @ Sun, 21 Jun 2020 18:59:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:59:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:59:48: #2 number of paired peaks: 1039 INFO @ Sun, 21 Jun 2020 18:59:48: start model_add_line... INFO @ Sun, 21 Jun 2020 18:59:49: start X-correlation... INFO @ Sun, 21 Jun 2020 18:59:49: end of X-cor INFO @ Sun, 21 Jun 2020 18:59:49: #2 finished! INFO @ Sun, 21 Jun 2020 18:59:49: #2 predicted fragment length is 88 bps INFO @ Sun, 21 Jun 2020 18:59:49: #2 alternative fragment length(s) may be 88,595 bps INFO @ Sun, 21 Jun 2020 18:59:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592476/SRX2592476.20_model.r WARNING @ Sun, 21 Jun 2020 18:59:49: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:59:49: #2 You may need to consider one of the other alternative d(s): 88,595 WARNING @ Sun, 21 Jun 2020 18:59:49: #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 18:59:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:59:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:59:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:00:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592476/SRX2592476.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:00:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592476/SRX2592476.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:00:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592476/SRX2592476.20_summits.bed INFO @ Sun, 21 Jun 2020 19:00:03: Done! pass1 - making usageList (165 chroms): 1 millis pass2 - checking and writing primary data (276 records, 4 fields): 6 millis CompletedMACS2peakCalling