Job ID = 6457850 SRX = SRX4801814 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:55:03 prefetch.2.10.7: 1) Downloading 'SRR7968399'... 2020-06-21T11:55:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:57:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:57:58 prefetch.2.10.7: 'SRR7968399' is valid 2020-06-21T11:57:58 prefetch.2.10.7: 1) 'SRR7968399' was downloaded successfully Read 13961446 spots for SRR7968399/SRR7968399.sra Written 13961446 spots for SRR7968399/SRR7968399.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: 00:04:31 13961446 reads; of these: 13961446 (100.00%) were unpaired; of these: 384028 (2.75%) aligned 0 times 9623042 (68.93%) aligned exactly 1 time 3954376 (28.32%) aligned >1 times 97.25% overall alignment rate Time searching: 00:04:31 Overall time: 00:04:31 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_sort_core] merging from 8 files... [bam_rmdupse_core] 1898864 / 13577418 = 0.1399 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 21:07:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4801814/SRX4801814.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4801814/SRX4801814.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4801814/SRX4801814.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4801814/SRX4801814.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 21:07:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:07:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:07:09: 1000000 INFO @ Sun, 21 Jun 2020 21:07:14: 2000000 INFO @ Sun, 21 Jun 2020 21:07:19: 3000000 INFO @ Sun, 21 Jun 2020 21:07:24: 4000000 INFO @ Sun, 21 Jun 2020 21:07:29: 5000000 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 21:07:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4801814/SRX4801814.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4801814/SRX4801814.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4801814/SRX4801814.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4801814/SRX4801814.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 21:07:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:07:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:07:34: 6000000 INFO @ Sun, 21 Jun 2020 21:07:39: 7000000 INFO @ Sun, 21 Jun 2020 21:07:40: 1000000 INFO @ Sun, 21 Jun 2020 21:07:44: 8000000 INFO @ Sun, 21 Jun 2020 21:07:46: 2000000 INFO @ Sun, 21 Jun 2020 21:07:49: 9000000 INFO @ Sun, 21 Jun 2020 21:07:52: 3000000 INFO @ Sun, 21 Jun 2020 21:07:54: 10000000 INFO @ Sun, 21 Jun 2020 21:07:58: 4000000 INFO @ Sun, 21 Jun 2020 21:07:59: 11000000 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 21:08:03: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 21:08:03: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 21:08:03: #1 total tags in treatment: 11678554 INFO @ Sun, 21 Jun 2020 21:08:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:08:03: #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 21:08:03: 5000000 INFO @ Sun, 21 Jun 2020 21:08:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4801814/SRX4801814.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4801814/SRX4801814.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4801814/SRX4801814.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4801814/SRX4801814.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 21:08:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:08:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:08:04: #1 tags after filtering in treatment: 11678435 INFO @ Sun, 21 Jun 2020 21:08:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:08:04: #1 finished! INFO @ Sun, 21 Jun 2020 21:08:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:08:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:08:04: #2 number of paired peaks: 2592 INFO @ Sun, 21 Jun 2020 21:08:04: start model_add_line... INFO @ Sun, 21 Jun 2020 21:08:05: start X-correlation... INFO @ Sun, 21 Jun 2020 21:08:05: end of X-cor INFO @ Sun, 21 Jun 2020 21:08:05: #2 finished! INFO @ Sun, 21 Jun 2020 21:08:05: #2 predicted fragment length is 145 bps INFO @ Sun, 21 Jun 2020 21:08:05: #2 alternative fragment length(s) may be 145 bps INFO @ Sun, 21 Jun 2020 21:08:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4801814/SRX4801814.05_model.r INFO @ Sun, 21 Jun 2020 21:08:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:08:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:08:09: 1000000 INFO @ Sun, 21 Jun 2020 21:08:09: 6000000 INFO @ Sun, 21 Jun 2020 21:08:14: 2000000 INFO @ Sun, 21 Jun 2020 21:08:15: 7000000 INFO @ Sun, 21 Jun 2020 21:08:19: 3000000 INFO @ Sun, 21 Jun 2020 21:08:21: 8000000 INFO @ Sun, 21 Jun 2020 21:08:24: 4000000 INFO @ Sun, 21 Jun 2020 21:08:27: 9000000 INFO @ Sun, 21 Jun 2020 21:08:29: 5000000 INFO @ Sun, 21 Jun 2020 21:08:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:08:33: 10000000 INFO @ Sun, 21 Jun 2020 21:08:35: 6000000 INFO @ Sun, 21 Jun 2020 21:08:39: 11000000 INFO @ Sun, 21 Jun 2020 21:08:40: 7000000 INFO @ Sun, 21 Jun 2020 21:08:43: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 21:08:43: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 21:08:43: #1 total tags in treatment: 11678554 INFO @ Sun, 21 Jun 2020 21:08:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:08:43: #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 21:08:44: #1 tags after filtering in treatment: 11678435 INFO @ Sun, 21 Jun 2020 21:08:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:08:44: #1 finished! INFO @ Sun, 21 Jun 2020 21:08:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:08:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:08:45: #2 number of paired peaks: 2592 INFO @ Sun, 21 Jun 2020 21:08:45: start model_add_line... INFO @ Sun, 21 Jun 2020 21:08:45: start X-correlation... INFO @ Sun, 21 Jun 2020 21:08:45: end of X-cor INFO @ Sun, 21 Jun 2020 21:08:45: #2 finished! INFO @ Sun, 21 Jun 2020 21:08:45: #2 predicted fragment length is 145 bps INFO @ Sun, 21 Jun 2020 21:08:45: #2 alternative fragment length(s) may be 145 bps INFO @ Sun, 21 Jun 2020 21:08:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4801814/SRX4801814.10_model.r INFO @ Sun, 21 Jun 2020 21:08:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:08:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:08:45: 8000000 INFO @ Sun, 21 Jun 2020 21:08:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4801814/SRX4801814.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:08:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4801814/SRX4801814.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:08:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4801814/SRX4801814.05_summits.bed INFO @ Sun, 21 Jun 2020 21:08:46: Done! pass1 - making usageList (570 chroms): 2 millis pass2 - checking and writing primary data (7152 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:08:50: 9000000 INFO @ Sun, 21 Jun 2020 21:08:55: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:09:00: 11000000 INFO @ Sun, 21 Jun 2020 21:09:04: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 21:09:04: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 21:09:04: #1 total tags in treatment: 11678554 INFO @ Sun, 21 Jun 2020 21:09:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:09:04: #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 21:09:04: #1 tags after filtering in treatment: 11678435 INFO @ Sun, 21 Jun 2020 21:09:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:09:04: #1 finished! INFO @ Sun, 21 Jun 2020 21:09:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:09:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:09:05: #2 number of paired peaks: 2592 INFO @ Sun, 21 Jun 2020 21:09:05: start model_add_line... INFO @ Sun, 21 Jun 2020 21:09:06: start X-correlation... INFO @ Sun, 21 Jun 2020 21:09:06: end of X-cor INFO @ Sun, 21 Jun 2020 21:09:06: #2 finished! INFO @ Sun, 21 Jun 2020 21:09:06: #2 predicted fragment length is 145 bps INFO @ Sun, 21 Jun 2020 21:09:06: #2 alternative fragment length(s) may be 145 bps INFO @ Sun, 21 Jun 2020 21:09:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4801814/SRX4801814.20_model.r INFO @ Sun, 21 Jun 2020 21:09:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:09:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:09:12: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:09:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4801814/SRX4801814.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:09:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4801814/SRX4801814.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:09:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4801814/SRX4801814.10_summits.bed INFO @ Sun, 21 Jun 2020 21:09:26: Done! pass1 - making usageList (498 chroms): 1 millis pass2 - checking and writing primary data (5132 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:09:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:09:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4801814/SRX4801814.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:09:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4801814/SRX4801814.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:09:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4801814/SRX4801814.20_summits.bed INFO @ Sun, 21 Jun 2020 21:09:48: Done! pass1 - making usageList (394 chroms): 1 millis pass2 - checking and writing primary data (3147 records, 4 fields): 14 millis CompletedMACS2peakCalling