Job ID = 14167464 SRX = ERX3978914 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 26447591 spots for ERR3975983/ERR3975983.sra Written 26447591 spots for ERR3975983/ERR3975983.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168338 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:10:58 26447591 reads; of these: 26447591 (100.00%) were paired; of these: 3355423 (12.69%) aligned concordantly 0 times 18799094 (71.08%) aligned concordantly exactly 1 time 4293074 (16.23%) aligned concordantly >1 times ---- 3355423 pairs aligned concordantly 0 times; of these: 711949 (21.22%) aligned discordantly 1 time ---- 2643474 pairs aligned 0 times concordantly or discordantly; of these: 5286948 mates make up the pairs; of these: 2592091 (49.03%) aligned 0 times 1473439 (27.87%) aligned exactly 1 time 1221418 (23.10%) aligned >1 times 95.10% overall alignment rate Time searching: 01:10:59 Overall time: 01:10:59 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 24 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] 16431486 / 23706245 = 0.6931 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 13:47:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978914/ERX3978914.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978914/ERX3978914.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978914/ERX3978914.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978914/ERX3978914.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 13:47:07: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:47:07: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:47:13: 1000000 INFO @ Fri, 10 Dec 2021 13:47:19: 2000000 INFO @ Fri, 10 Dec 2021 13:47:25: 3000000 INFO @ Fri, 10 Dec 2021 13:47:31: 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 13:47:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978914/ERX3978914.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978914/ERX3978914.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978914/ERX3978914.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978914/ERX3978914.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 13:47:37: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:47:37: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:47:37: 5000000 INFO @ Fri, 10 Dec 2021 13:47:43: 1000000 INFO @ Fri, 10 Dec 2021 13:47:44: 6000000 INFO @ Fri, 10 Dec 2021 13:47:49: 2000000 INFO @ Fri, 10 Dec 2021 13:47:50: 7000000 INFO @ Fri, 10 Dec 2021 13:47:55: 3000000 INFO @ Fri, 10 Dec 2021 13:47:56: 8000000 INFO @ Fri, 10 Dec 2021 13:48:02: 4000000 INFO @ Fri, 10 Dec 2021 13:48:02: 9000000 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 13:48:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978914/ERX3978914.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978914/ERX3978914.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978914/ERX3978914.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978914/ERX3978914.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 13:48:07: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:48:07: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:48:08: 5000000 INFO @ Fri, 10 Dec 2021 13:48:08: 10000000 INFO @ Fri, 10 Dec 2021 13:48:13: 1000000 INFO @ Fri, 10 Dec 2021 13:48:14: 6000000 INFO @ Fri, 10 Dec 2021 13:48:14: 11000000 INFO @ Fri, 10 Dec 2021 13:48:19: 2000000 INFO @ Fri, 10 Dec 2021 13:48:20: 7000000 INFO @ Fri, 10 Dec 2021 13:48:20: 12000000 INFO @ Fri, 10 Dec 2021 13:48:26: 3000000 INFO @ Fri, 10 Dec 2021 13:48:26: 8000000 INFO @ Fri, 10 Dec 2021 13:48:27: 13000000 INFO @ Fri, 10 Dec 2021 13:48:32: 4000000 INFO @ Fri, 10 Dec 2021 13:48:33: 9000000 INFO @ Fri, 10 Dec 2021 13:48:33: 14000000 INFO @ Fri, 10 Dec 2021 13:48:38: 5000000 INFO @ Fri, 10 Dec 2021 13:48:39: 10000000 INFO @ Fri, 10 Dec 2021 13:48:39: 15000000 INFO @ Fri, 10 Dec 2021 13:48:44: 11000000 INFO @ Fri, 10 Dec 2021 13:48:45: 6000000 INFO @ Fri, 10 Dec 2021 13:48:45: 16000000 INFO @ Fri, 10 Dec 2021 13:48:50: 12000000 INFO @ Fri, 10 Dec 2021 13:48:51: 17000000 INFO @ Fri, 10 Dec 2021 13:48:51: 7000000 INFO @ Fri, 10 Dec 2021 13:48:54: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 13:48:54: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 13:48:54: #1 total tags in treatment: 7101930 INFO @ Fri, 10 Dec 2021 13:48:54: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:48:54: #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 13:48:54: #1 tags after filtering in treatment: 6198749 INFO @ Fri, 10 Dec 2021 13:48:54: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 10 Dec 2021 13:48:54: #1 finished! INFO @ Fri, 10 Dec 2021 13:48:54: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:48:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:48:54: #2 number of paired peaks: 6841 INFO @ Fri, 10 Dec 2021 13:48:54: start model_add_line... INFO @ Fri, 10 Dec 2021 13:48:55: start X-correlation... INFO @ Fri, 10 Dec 2021 13:48:55: end of X-cor INFO @ Fri, 10 Dec 2021 13:48:55: #2 finished! INFO @ Fri, 10 Dec 2021 13:48:55: #2 predicted fragment length is 192 bps INFO @ Fri, 10 Dec 2021 13:48:55: #2 alternative fragment length(s) may be 192 bps INFO @ Fri, 10 Dec 2021 13:48:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978914/ERX3978914.05_model.r INFO @ Fri, 10 Dec 2021 13:48:55: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:48:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:48:56: 13000000 INFO @ Fri, 10 Dec 2021 13:48:57: 8000000 INFO @ Fri, 10 Dec 2021 13:49:03: 14000000 INFO @ Fri, 10 Dec 2021 13:49:04: 9000000 INFO @ Fri, 10 Dec 2021 13:49:09: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:49:09: 15000000 INFO @ Fri, 10 Dec 2021 13:49:10: 10000000 INFO @ Fri, 10 Dec 2021 13:49:15: 16000000 INFO @ Fri, 10 Dec 2021 13:49:16: 11000000 INFO @ Fri, 10 Dec 2021 13:49:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978914/ERX3978914.05_peaks.xls INFO @ Fri, 10 Dec 2021 13:49:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978914/ERX3978914.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:49:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978914/ERX3978914.05_summits.bed INFO @ Fri, 10 Dec 2021 13:49:16: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9361 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 13:49:20: 17000000 INFO @ Fri, 10 Dec 2021 13:49:22: 12000000 INFO @ Fri, 10 Dec 2021 13:49:23: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 13:49:23: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 13:49:23: #1 total tags in treatment: 7101930 INFO @ Fri, 10 Dec 2021 13:49:23: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:49:23: #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 13:49:23: #1 tags after filtering in treatment: 6198749 INFO @ Fri, 10 Dec 2021 13:49:23: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 10 Dec 2021 13:49:23: #1 finished! INFO @ Fri, 10 Dec 2021 13:49:23: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:49:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:49:24: #2 number of paired peaks: 6841 INFO @ Fri, 10 Dec 2021 13:49:24: start model_add_line... INFO @ Fri, 10 Dec 2021 13:49:24: start X-correlation... INFO @ Fri, 10 Dec 2021 13:49:24: end of X-cor INFO @ Fri, 10 Dec 2021 13:49:24: #2 finished! INFO @ Fri, 10 Dec 2021 13:49:24: #2 predicted fragment length is 192 bps INFO @ Fri, 10 Dec 2021 13:49:24: #2 alternative fragment length(s) may be 192 bps INFO @ Fri, 10 Dec 2021 13:49:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978914/ERX3978914.10_model.r INFO @ Fri, 10 Dec 2021 13:49:24: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:49:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:49:28: 13000000 INFO @ Fri, 10 Dec 2021 13:49:33: 14000000 INFO @ Fri, 10 Dec 2021 13:49:39: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:49:39: 15000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 13:49:45: 16000000 INFO @ Fri, 10 Dec 2021 13:49:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978914/ERX3978914.10_peaks.xls INFO @ Fri, 10 Dec 2021 13:49:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978914/ERX3978914.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:49:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978914/ERX3978914.10_summits.bed INFO @ Fri, 10 Dec 2021 13:49:46: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7123 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:49:51: 17000000 INFO @ Fri, 10 Dec 2021 13:49:54: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 13:49:54: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 13:49:54: #1 total tags in treatment: 7101930 INFO @ Fri, 10 Dec 2021 13:49:54: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:49:54: #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 13:49:54: #1 tags after filtering in treatment: 6198749 INFO @ Fri, 10 Dec 2021 13:49:54: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 10 Dec 2021 13:49:54: #1 finished! INFO @ Fri, 10 Dec 2021 13:49:54: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:49:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:49:54: #2 number of paired peaks: 6841 INFO @ Fri, 10 Dec 2021 13:49:54: start model_add_line... INFO @ Fri, 10 Dec 2021 13:49:55: start X-correlation... INFO @ Fri, 10 Dec 2021 13:49:55: end of X-cor INFO @ Fri, 10 Dec 2021 13:49:55: #2 finished! INFO @ Fri, 10 Dec 2021 13:49:55: #2 predicted fragment length is 192 bps INFO @ Fri, 10 Dec 2021 13:49:55: #2 alternative fragment length(s) may be 192 bps INFO @ Fri, 10 Dec 2021 13:49:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978914/ERX3978914.20_model.r INFO @ Fri, 10 Dec 2021 13:49:55: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:49:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:50:09: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:50:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978914/ERX3978914.20_peaks.xls INFO @ Fri, 10 Dec 2021 13:50:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978914/ERX3978914.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:50:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978914/ERX3978914.20_summits.bed INFO @ Fri, 10 Dec 2021 13:50:16: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5444 records, 4 fields): 7 millis CompletedMACS2peakCalling