Job ID = 14172080 SRX = SRX7628900 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 29767092 spots for SRR10963262/SRR10963262.sra Written 29767092 spots for SRR10963262/SRR10963262.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172565 ("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: 00:18:48 29767092 reads; of these: 29767092 (100.00%) were paired; of these: 22906631 (76.95%) aligned concordantly 0 times 5134102 (17.25%) aligned concordantly exactly 1 time 1726359 (5.80%) aligned concordantly >1 times ---- 22906631 pairs aligned concordantly 0 times; of these: 131683 (0.57%) aligned discordantly 1 time ---- 22774948 pairs aligned 0 times concordantly or discordantly; of these: 45549896 mates make up the pairs; of these: 45239325 (99.32%) aligned 0 times 167161 (0.37%) aligned exactly 1 time 143410 (0.31%) aligned >1 times 24.01% overall alignment rate Time searching: 00:18:49 Overall time: 00:18:49 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] 1156436 / 6987627 = 0.1655 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 @ Sat, 11 Dec 2021 14:27:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628900/SRX7628900.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628900/SRX7628900.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628900/SRX7628900.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628900/SRX7628900.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 @ Sat, 11 Dec 2021 14:27:34: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:27:34: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:27:40: 1000000 INFO @ Sat, 11 Dec 2021 14:27:46: 2000000 INFO @ Sat, 11 Dec 2021 14:27:52: 3000000 INFO @ Sat, 11 Dec 2021 14:27:58: 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 @ Sat, 11 Dec 2021 14:28:04: 5000000 INFO @ Sat, 11 Dec 2021 14:28:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628900/SRX7628900.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628900/SRX7628900.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628900/SRX7628900.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628900/SRX7628900.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 @ Sat, 11 Dec 2021 14:28:04: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:28:04: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:28:10: 1000000 INFO @ Sat, 11 Dec 2021 14:28:10: 6000000 INFO @ Sat, 11 Dec 2021 14:28:16: 2000000 INFO @ Sat, 11 Dec 2021 14:28:16: 7000000 INFO @ Sat, 11 Dec 2021 14:28:22: 3000000 INFO @ Sat, 11 Dec 2021 14:28:23: 8000000 INFO @ Sat, 11 Dec 2021 14:28:28: 4000000 INFO @ Sat, 11 Dec 2021 14:28:29: 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 @ Sat, 11 Dec 2021 14:28:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628900/SRX7628900.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628900/SRX7628900.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628900/SRX7628900.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628900/SRX7628900.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 @ Sat, 11 Dec 2021 14:28:34: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:28:34: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:28:34: 5000000 INFO @ Sat, 11 Dec 2021 14:28:35: 10000000 INFO @ Sat, 11 Dec 2021 14:28:41: 6000000 INFO @ Sat, 11 Dec 2021 14:28:41: 1000000 INFO @ Sat, 11 Dec 2021 14:28:41: 11000000 INFO @ Sat, 11 Dec 2021 14:28:47: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 14:28:47: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 14:28:47: #1 total tags in treatment: 5710776 INFO @ Sat, 11 Dec 2021 14:28:47: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:28:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 14:28:47: #1 tags after filtering in treatment: 5140348 INFO @ Sat, 11 Dec 2021 14:28:47: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 11 Dec 2021 14:28:47: #1 finished! INFO @ Sat, 11 Dec 2021 14:28:47: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:28:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:28:47: 7000000 INFO @ Sat, 11 Dec 2021 14:28:48: #2 number of paired peaks: 1439 INFO @ Sat, 11 Dec 2021 14:28:48: start model_add_line... INFO @ Sat, 11 Dec 2021 14:28:48: 2000000 INFO @ Sat, 11 Dec 2021 14:28:48: start X-correlation... INFO @ Sat, 11 Dec 2021 14:28:48: end of X-cor INFO @ Sat, 11 Dec 2021 14:28:48: #2 finished! INFO @ Sat, 11 Dec 2021 14:28:48: #2 predicted fragment length is 141 bps INFO @ Sat, 11 Dec 2021 14:28:48: #2 alternative fragment length(s) may be 141 bps INFO @ Sat, 11 Dec 2021 14:28:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628900/SRX7628900.05_model.r INFO @ Sat, 11 Dec 2021 14:28:48: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:28:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:28:54: 8000000 INFO @ Sat, 11 Dec 2021 14:28:54: 3000000 INFO @ Sat, 11 Dec 2021 14:28:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:29:01: 9000000 INFO @ Sat, 11 Dec 2021 14:29:01: 4000000 INFO @ Sat, 11 Dec 2021 14:29:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628900/SRX7628900.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:29:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628900/SRX7628900.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:29:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628900/SRX7628900.05_summits.bed INFO @ Sat, 11 Dec 2021 14:29:05: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4839 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:29:07: 10000000 INFO @ Sat, 11 Dec 2021 14:29:08: 5000000 INFO @ Sat, 11 Dec 2021 14:29:14: 11000000 INFO @ Sat, 11 Dec 2021 14:29:14: 6000000 INFO @ Sat, 11 Dec 2021 14:29:20: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 14:29:20: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 14:29:20: #1 total tags in treatment: 5710776 INFO @ Sat, 11 Dec 2021 14:29:20: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:29:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 14:29:20: #1 tags after filtering in treatment: 5140348 INFO @ Sat, 11 Dec 2021 14:29:20: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 11 Dec 2021 14:29:20: #1 finished! INFO @ Sat, 11 Dec 2021 14:29:20: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:29:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:29:21: #2 number of paired peaks: 1439 INFO @ Sat, 11 Dec 2021 14:29:21: start model_add_line... INFO @ Sat, 11 Dec 2021 14:29:21: start X-correlation... INFO @ Sat, 11 Dec 2021 14:29:21: end of X-cor INFO @ Sat, 11 Dec 2021 14:29:21: #2 finished! INFO @ Sat, 11 Dec 2021 14:29:21: #2 predicted fragment length is 141 bps INFO @ Sat, 11 Dec 2021 14:29:21: #2 alternative fragment length(s) may be 141 bps INFO @ Sat, 11 Dec 2021 14:29:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628900/SRX7628900.10_model.r INFO @ Sat, 11 Dec 2021 14:29:21: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:29:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:29:21: 7000000 INFO @ Sat, 11 Dec 2021 14:29:27: 8000000 INFO @ Sat, 11 Dec 2021 14:29:32: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:29:33: 9000000 INFO @ Sat, 11 Dec 2021 14:29:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628900/SRX7628900.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:29:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628900/SRX7628900.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:29:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628900/SRX7628900.10_summits.bed INFO @ Sat, 11 Dec 2021 14:29:38: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1629 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:29:39: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:29:45: 11000000 INFO @ Sat, 11 Dec 2021 14:29:50: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 14:29:50: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 14:29:50: #1 total tags in treatment: 5710776 INFO @ Sat, 11 Dec 2021 14:29:50: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:29:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 14:29:50: #1 tags after filtering in treatment: 5140348 INFO @ Sat, 11 Dec 2021 14:29:50: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 11 Dec 2021 14:29:50: #1 finished! INFO @ Sat, 11 Dec 2021 14:29:50: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:29:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:29:51: #2 number of paired peaks: 1439 INFO @ Sat, 11 Dec 2021 14:29:51: start model_add_line... INFO @ Sat, 11 Dec 2021 14:29:51: start X-correlation... INFO @ Sat, 11 Dec 2021 14:29:51: end of X-cor INFO @ Sat, 11 Dec 2021 14:29:51: #2 finished! INFO @ Sat, 11 Dec 2021 14:29:51: #2 predicted fragment length is 141 bps INFO @ Sat, 11 Dec 2021 14:29:51: #2 alternative fragment length(s) may be 141 bps INFO @ Sat, 11 Dec 2021 14:29:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628900/SRX7628900.20_model.r INFO @ Sat, 11 Dec 2021 14:29:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:29:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:30:01: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:30:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628900/SRX7628900.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:30:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628900/SRX7628900.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:30:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628900/SRX7628900.20_summits.bed INFO @ Sat, 11 Dec 2021 14:30:07: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (493 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。