Job ID = 14167194 SRX = SRX10760659 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 16428574 spots for SRR14408510/SRR14408510.sra Written 16428574 spots for SRR14408510/SRR14408510.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167741 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:57 16428574 reads; of these: 16428574 (100.00%) were unpaired; of these: 4496089 (27.37%) aligned 0 times 10704280 (65.16%) aligned exactly 1 time 1228205 (7.48%) aligned >1 times 72.63% overall alignment rate Time searching: 00:03:57 Overall time: 00:03:57 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2984489 / 11932485 = 0.2501 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 11:04:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10760659/SRX10760659.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10760659/SRX10760659.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10760659/SRX10760659.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10760659/SRX10760659.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 @ Fri, 10 Dec 2021 11:04:20: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:04:20: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:04:26: 1000000 INFO @ Fri, 10 Dec 2021 11:04:32: 2000000 INFO @ Fri, 10 Dec 2021 11:04:38: 3000000 INFO @ Fri, 10 Dec 2021 11:04:44: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 11:04:49: 5000000 INFO @ Fri, 10 Dec 2021 11:04:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10760659/SRX10760659.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10760659/SRX10760659.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10760659/SRX10760659.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10760659/SRX10760659.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 @ Fri, 10 Dec 2021 11:04:50: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:04:50: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:04:56: 6000000 INFO @ Fri, 10 Dec 2021 11:04:59: 1000000 INFO @ Fri, 10 Dec 2021 11:05:03: 7000000 INFO @ Fri, 10 Dec 2021 11:05:06: 2000000 INFO @ Fri, 10 Dec 2021 11:05:10: 8000000 INFO @ Fri, 10 Dec 2021 11:05:14: 3000000 INFO @ Fri, 10 Dec 2021 11:05:17: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 11:05:17: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 11:05:17: #1 total tags in treatment: 8947996 INFO @ Fri, 10 Dec 2021 11:05:17: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:05:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:05:17: #1 tags after filtering in treatment: 8947996 INFO @ Fri, 10 Dec 2021 11:05:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:05:17: #1 finished! INFO @ Fri, 10 Dec 2021 11:05:17: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:05:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:05:18: #2 number of paired peaks: 7113 INFO @ Fri, 10 Dec 2021 11:05:18: start model_add_line... INFO @ Fri, 10 Dec 2021 11:05:18: start X-correlation... INFO @ Fri, 10 Dec 2021 11:05:18: end of X-cor INFO @ Fri, 10 Dec 2021 11:05:18: #2 finished! INFO @ Fri, 10 Dec 2021 11:05:18: #2 predicted fragment length is 180 bps INFO @ Fri, 10 Dec 2021 11:05:18: #2 alternative fragment length(s) may be 180 bps INFO @ Fri, 10 Dec 2021 11:05:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10760659/SRX10760659.05_model.r INFO @ Fri, 10 Dec 2021 11:05:18: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:05:18: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 11:05:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10760659/SRX10760659.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10760659/SRX10760659.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10760659/SRX10760659.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10760659/SRX10760659.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 @ Fri, 10 Dec 2021 11:05:20: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:05:20: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:05:22: 4000000 INFO @ Fri, 10 Dec 2021 11:05:28: 1000000 INFO @ Fri, 10 Dec 2021 11:05:29: 5000000 INFO @ Fri, 10 Dec 2021 11:05:35: 2000000 INFO @ Fri, 10 Dec 2021 11:05:37: 6000000 INFO @ Fri, 10 Dec 2021 11:05:41: 3000000 INFO @ Fri, 10 Dec 2021 11:05:42: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:05:45: 7000000 INFO @ Fri, 10 Dec 2021 11:05:48: 4000000 INFO @ Fri, 10 Dec 2021 11:05:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10760659/SRX10760659.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:05:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10760659/SRX10760659.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:05:52: 8000000 INFO @ Fri, 10 Dec 2021 11:05:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10760659/SRX10760659.05_summits.bed INFO @ Fri, 10 Dec 2021 11:05:52: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (13883 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:05:55: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:06:00: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 11:06:00: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 11:06:00: #1 total tags in treatment: 8947996 INFO @ Fri, 10 Dec 2021 11:06:00: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:06:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:06:00: #1 tags after filtering in treatment: 8947996 INFO @ Fri, 10 Dec 2021 11:06:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:06:00: #1 finished! INFO @ Fri, 10 Dec 2021 11:06:00: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:06:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:06:01: #2 number of paired peaks: 7113 INFO @ Fri, 10 Dec 2021 11:06:01: start model_add_line... INFO @ Fri, 10 Dec 2021 11:06:01: start X-correlation... INFO @ Fri, 10 Dec 2021 11:06:01: end of X-cor INFO @ Fri, 10 Dec 2021 11:06:01: #2 finished! INFO @ Fri, 10 Dec 2021 11:06:01: #2 predicted fragment length is 180 bps INFO @ Fri, 10 Dec 2021 11:06:01: #2 alternative fragment length(s) may be 180 bps INFO @ Fri, 10 Dec 2021 11:06:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10760659/SRX10760659.10_model.r INFO @ Fri, 10 Dec 2021 11:06:01: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:06:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:06:02: 6000000 INFO @ Fri, 10 Dec 2021 11:06:09: 7000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:06:15: 8000000 INFO @ Fri, 10 Dec 2021 11:06:21: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 11:06:21: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 11:06:21: #1 total tags in treatment: 8947996 INFO @ Fri, 10 Dec 2021 11:06:21: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:06:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:06:21: #1 tags after filtering in treatment: 8947996 INFO @ Fri, 10 Dec 2021 11:06:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:06:21: #1 finished! INFO @ Fri, 10 Dec 2021 11:06:21: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:06:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:06:23: #2 number of paired peaks: 7113 INFO @ Fri, 10 Dec 2021 11:06:23: start model_add_line... INFO @ Fri, 10 Dec 2021 11:06:23: start X-correlation... INFO @ Fri, 10 Dec 2021 11:06:23: end of X-cor INFO @ Fri, 10 Dec 2021 11:06:23: #2 finished! INFO @ Fri, 10 Dec 2021 11:06:23: #2 predicted fragment length is 180 bps INFO @ Fri, 10 Dec 2021 11:06:23: #2 alternative fragment length(s) may be 180 bps INFO @ Fri, 10 Dec 2021 11:06:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10760659/SRX10760659.20_model.r INFO @ Fri, 10 Dec 2021 11:06:23: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:06:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:06:24: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:06:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10760659/SRX10760659.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:06:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10760659/SRX10760659.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:06:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10760659/SRX10760659.10_summits.bed INFO @ Fri, 10 Dec 2021 11:06:35: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9626 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:06:46: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:06:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10760659/SRX10760659.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:06:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10760659/SRX10760659.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:06:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10760659/SRX10760659.20_summits.bed INFO @ Fri, 10 Dec 2021 11:06:56: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6422 records, 4 fields): 7 millis CompletedMACS2peakCalling