Job ID = 14168448 SRX = ERX3978869 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5985763 spots for ERR3975938/ERR3975938.sra Written 5985763 spots for ERR3975938/ERR3975938.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169607 ("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: 00:12:27 5985763 reads; of these: 5985763 (100.00%) were paired; of these: 759970 (12.70%) aligned concordantly 0 times 4301309 (71.86%) aligned concordantly exactly 1 time 924484 (15.44%) aligned concordantly >1 times ---- 759970 pairs aligned concordantly 0 times; of these: 109082 (14.35%) aligned discordantly 1 time ---- 650888 pairs aligned 0 times concordantly or discordantly; of these: 1301776 mates make up the pairs; of these: 848838 (65.21%) aligned 0 times 210379 (16.16%) aligned exactly 1 time 242559 (18.63%) aligned >1 times 92.91% overall alignment rate Time searching: 00:12:27 Overall time: 00:12:27 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 3622602 / 5319627 = 0.6810 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 18:43:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978869/ERX3978869.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978869/ERX3978869.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978869/ERX3978869.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978869/ERX3978869.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 18:43:13: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:43:13: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:43:19: 1000000 INFO @ Fri, 10 Dec 2021 18:43:24: 2000000 INFO @ Fri, 10 Dec 2021 18:43:29: 3000000 INFO @ Fri, 10 Dec 2021 18:43:34: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 18:43:34: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 18:43:34: #1 total tags in treatment: 1678571 INFO @ Fri, 10 Dec 2021 18:43:34: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:43:34: #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 18:43:34: #1 tags after filtering in treatment: 1616062 INFO @ Fri, 10 Dec 2021 18:43:34: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 10 Dec 2021 18:43:34: #1 finished! INFO @ Fri, 10 Dec 2021 18:43:34: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:43:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:43:34: #2 number of paired peaks: 1437 INFO @ Fri, 10 Dec 2021 18:43:34: start model_add_line... INFO @ Fri, 10 Dec 2021 18:43:34: start X-correlation... INFO @ Fri, 10 Dec 2021 18:43:34: end of X-cor INFO @ Fri, 10 Dec 2021 18:43:34: #2 finished! INFO @ Fri, 10 Dec 2021 18:43:34: #2 predicted fragment length is 181 bps INFO @ Fri, 10 Dec 2021 18:43:34: #2 alternative fragment length(s) may be 181 bps INFO @ Fri, 10 Dec 2021 18:43:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978869/ERX3978869.05_model.r INFO @ Fri, 10 Dec 2021 18:43:34: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:43:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:43:38: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:43:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978869/ERX3978869.05_peaks.xls INFO @ Fri, 10 Dec 2021 18:43:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978869/ERX3978869.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:43:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978869/ERX3978869.05_summits.bed INFO @ Fri, 10 Dec 2021 18:43:39: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1479 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 18:43:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978869/ERX3978869.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978869/ERX3978869.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978869/ERX3978869.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978869/ERX3978869.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 18:43:43: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:43:43: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:43:48: 1000000 INFO @ Fri, 10 Dec 2021 18:43:53: 2000000 INFO @ Fri, 10 Dec 2021 18:43:59: 3000000 INFO @ Fri, 10 Dec 2021 18:44:03: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 18:44:03: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 18:44:03: #1 total tags in treatment: 1678571 INFO @ Fri, 10 Dec 2021 18:44:03: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:44:03: #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 18:44:03: #1 tags after filtering in treatment: 1616062 INFO @ Fri, 10 Dec 2021 18:44:03: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 10 Dec 2021 18:44:03: #1 finished! INFO @ Fri, 10 Dec 2021 18:44:03: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:44:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:44:03: #2 number of paired peaks: 1437 INFO @ Fri, 10 Dec 2021 18:44:03: start model_add_line... INFO @ Fri, 10 Dec 2021 18:44:03: start X-correlation... INFO @ Fri, 10 Dec 2021 18:44:03: end of X-cor INFO @ Fri, 10 Dec 2021 18:44:03: #2 finished! INFO @ Fri, 10 Dec 2021 18:44:03: #2 predicted fragment length is 181 bps INFO @ Fri, 10 Dec 2021 18:44:03: #2 alternative fragment length(s) may be 181 bps INFO @ Fri, 10 Dec 2021 18:44:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978869/ERX3978869.10_model.r INFO @ Fri, 10 Dec 2021 18:44:03: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:44:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:44:07: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:44:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978869/ERX3978869.10_peaks.xls INFO @ Fri, 10 Dec 2021 18:44:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978869/ERX3978869.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:44:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978869/ERX3978869.10_summits.bed INFO @ Fri, 10 Dec 2021 18:44:09: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (560 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 18:44:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978869/ERX3978869.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978869/ERX3978869.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978869/ERX3978869.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978869/ERX3978869.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 18:44:13: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:44:13: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:44:19: 1000000 INFO @ Fri, 10 Dec 2021 18:44:25: 2000000 INFO @ Fri, 10 Dec 2021 18:44:31: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 18:44:37: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 18:44:37: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 18:44:37: #1 total tags in treatment: 1678571 INFO @ Fri, 10 Dec 2021 18:44:37: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:44:37: #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 18:44:37: #1 tags after filtering in treatment: 1616062 INFO @ Fri, 10 Dec 2021 18:44:37: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 10 Dec 2021 18:44:37: #1 finished! INFO @ Fri, 10 Dec 2021 18:44:37: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:44:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:44:37: #2 number of paired peaks: 1437 INFO @ Fri, 10 Dec 2021 18:44:37: start model_add_line... INFO @ Fri, 10 Dec 2021 18:44:37: start X-correlation... INFO @ Fri, 10 Dec 2021 18:44:37: end of X-cor INFO @ Fri, 10 Dec 2021 18:44:37: #2 finished! INFO @ Fri, 10 Dec 2021 18:44:37: #2 predicted fragment length is 181 bps INFO @ Fri, 10 Dec 2021 18:44:37: #2 alternative fragment length(s) may be 181 bps INFO @ Fri, 10 Dec 2021 18:44:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978869/ERX3978869.20_model.r INFO @ Fri, 10 Dec 2021 18:44:37: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:44:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:44:41: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 18:44:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978869/ERX3978869.20_peaks.xls INFO @ Fri, 10 Dec 2021 18:44:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978869/ERX3978869.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:44:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978869/ERX3978869.20_summits.bed INFO @ Fri, 10 Dec 2021 18:44:42: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (221 records, 4 fields): 2 millis CompletedMACS2peakCalling