Job ID = 6454083 SRX = SRX181428 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:58:04 prefetch.2.10.7: 1) Downloading 'SRR548165'... 2020-06-21T08:58:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:00:27 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:00:27 prefetch.2.10.7: 'SRR548165' is valid 2020-06-21T09:00:27 prefetch.2.10.7: 1) 'SRR548165' was downloaded successfully Read 22148792 spots for SRR548165/SRR548165.sra Written 22148792 spots for SRR548165/SRR548165.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: 00:03:06 22148792 reads; of these: 22148792 (100.00%) were unpaired; of these: 10957141 (49.47%) aligned 0 times 10056139 (45.40%) aligned exactly 1 time 1135512 (5.13%) aligned >1 times 50.53% overall alignment rate Time searching: 00:03:06 Overall time: 00:03:06 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] 7934003 / 11191651 = 0.7089 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 18:06:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX181428/SRX181428.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX181428/SRX181428.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX181428/SRX181428.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX181428/SRX181428.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 18:06:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:06:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:06:46: 1000000 INFO @ Sun, 21 Jun 2020 18:06:52: 2000000 INFO @ Sun, 21 Jun 2020 18:06:58: 3000000 INFO @ Sun, 21 Jun 2020 18:07:00: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:07:00: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:07:00: #1 total tags in treatment: 3257648 INFO @ Sun, 21 Jun 2020 18:07:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:07:00: #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 18:07:00: #1 tags after filtering in treatment: 3257464 INFO @ Sun, 21 Jun 2020 18:07:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:07:00: #1 finished! INFO @ Sun, 21 Jun 2020 18:07:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:07:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:07:00: #2 number of paired peaks: 1955 INFO @ Sun, 21 Jun 2020 18:07:00: start model_add_line... INFO @ Sun, 21 Jun 2020 18:07:00: start X-correlation... INFO @ Sun, 21 Jun 2020 18:07:00: end of X-cor INFO @ Sun, 21 Jun 2020 18:07:00: #2 finished! INFO @ Sun, 21 Jun 2020 18:07:00: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 18:07:00: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 21 Jun 2020 18:07:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX181428/SRX181428.05_model.r INFO @ Sun, 21 Jun 2020 18:07:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:07:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:07:08: #3 Call peaks for each chromosome... 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 18:07:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX181428/SRX181428.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX181428/SRX181428.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX181428/SRX181428.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX181428/SRX181428.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 18:07:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:07:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:07:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX181428/SRX181428.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:07:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX181428/SRX181428.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:07:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX181428/SRX181428.05_summits.bed INFO @ Sun, 21 Jun 2020 18:07:12: Done! pass1 - making usageList (375 chroms): 2 millis pass2 - checking and writing primary data (3526 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:07:17: 1000000 INFO @ Sun, 21 Jun 2020 18:07:22: 2000000 INFO @ Sun, 21 Jun 2020 18:07:29: 3000000 INFO @ Sun, 21 Jun 2020 18:07:30: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:07:30: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:07:30: #1 total tags in treatment: 3257648 INFO @ Sun, 21 Jun 2020 18:07:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:07:30: #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 18:07:31: #1 tags after filtering in treatment: 3257464 INFO @ Sun, 21 Jun 2020 18:07:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:07:31: #1 finished! INFO @ Sun, 21 Jun 2020 18:07:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:07:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:07:31: #2 number of paired peaks: 1955 INFO @ Sun, 21 Jun 2020 18:07:31: start model_add_line... INFO @ Sun, 21 Jun 2020 18:07:31: start X-correlation... INFO @ Sun, 21 Jun 2020 18:07:31: end of X-cor INFO @ Sun, 21 Jun 2020 18:07:31: #2 finished! INFO @ Sun, 21 Jun 2020 18:07:31: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 18:07:31: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 21 Jun 2020 18:07:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX181428/SRX181428.10_model.r INFO @ Sun, 21 Jun 2020 18:07:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:07:31: #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 18:07:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:07:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX181428/SRX181428.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX181428/SRX181428.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX181428/SRX181428.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX181428/SRX181428.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 18:07:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:07:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:07:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX181428/SRX181428.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:07:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX181428/SRX181428.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:07:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX181428/SRX181428.10_summits.bed INFO @ Sun, 21 Jun 2020 18:07:43: Done! pass1 - making usageList (210 chroms): 1 millis pass2 - checking and writing primary data (932 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:07:46: 1000000 INFO @ Sun, 21 Jun 2020 18:07:52: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:07:57: 3000000 INFO @ Sun, 21 Jun 2020 18:07:59: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:07:59: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:07:59: #1 total tags in treatment: 3257648 INFO @ Sun, 21 Jun 2020 18:07:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:07:59: #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 18:07:59: #1 tags after filtering in treatment: 3257464 INFO @ Sun, 21 Jun 2020 18:07:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:07:59: #1 finished! INFO @ Sun, 21 Jun 2020 18:07:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:07:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:07:59: #2 number of paired peaks: 1955 INFO @ Sun, 21 Jun 2020 18:07:59: start model_add_line... INFO @ Sun, 21 Jun 2020 18:07:59: start X-correlation... INFO @ Sun, 21 Jun 2020 18:07:59: end of X-cor INFO @ Sun, 21 Jun 2020 18:07:59: #2 finished! INFO @ Sun, 21 Jun 2020 18:07:59: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 18:07:59: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 21 Jun 2020 18:07:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX181428/SRX181428.20_model.r INFO @ Sun, 21 Jun 2020 18:08:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:08:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:08:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:08:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX181428/SRX181428.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:08:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX181428/SRX181428.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:08:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX181428/SRX181428.20_summits.bed INFO @ Sun, 21 Jun 2020 18:08:11: Done! pass1 - making usageList (55 chroms): 1 millis pass2 - checking and writing primary data (129 records, 4 fields): 3 millis CompletedMACS2peakCalling