Job ID = 14171325 SRX = SRX9005674 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9763477 spots for SRR12515075/SRR12515075.sra Written 9763477 spots for SRR12515075/SRR12515075.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171889 ("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: 00:23:20 9763477 reads; of these: 9763477 (100.00%) were paired; of these: 439972 (4.51%) aligned concordantly 0 times 6509283 (66.67%) aligned concordantly exactly 1 time 2814222 (28.82%) aligned concordantly >1 times ---- 439972 pairs aligned concordantly 0 times; of these: 17018 (3.87%) aligned discordantly 1 time ---- 422954 pairs aligned 0 times concordantly or discordantly; of these: 845908 mates make up the pairs; of these: 523626 (61.90%) aligned 0 times 205279 (24.27%) aligned exactly 1 time 117003 (13.83%) aligned >1 times 97.32% overall alignment rate Time searching: 00:23:20 Overall time: 00:23:20 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] 1043817 / 9324989 = 0.1119 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 11:44:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005674/SRX9005674.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005674/SRX9005674.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005674/SRX9005674.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005674/SRX9005674.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 11:44:30: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:44:30: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:44:37: 1000000 INFO @ Sat, 11 Dec 2021 11:44:43: 2000000 INFO @ Sat, 11 Dec 2021 11:44:49: 3000000 INFO @ Sat, 11 Dec 2021 11:44:55: 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 11:45:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005674/SRX9005674.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005674/SRX9005674.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005674/SRX9005674.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005674/SRX9005674.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 11:45:00: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:45:00: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:45:01: 5000000 INFO @ Sat, 11 Dec 2021 11:45:07: 1000000 INFO @ Sat, 11 Dec 2021 11:45:08: 6000000 INFO @ Sat, 11 Dec 2021 11:45:14: 2000000 INFO @ Sat, 11 Dec 2021 11:45:15: 7000000 INFO @ Sat, 11 Dec 2021 11:45:21: 3000000 INFO @ Sat, 11 Dec 2021 11:45:22: 8000000 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 11:45:29: 4000000 INFO @ Sat, 11 Dec 2021 11:45:30: 9000000 INFO @ Sat, 11 Dec 2021 11:45:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005674/SRX9005674.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005674/SRX9005674.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005674/SRX9005674.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005674/SRX9005674.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 11:45:30: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:45:30: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:45:36: 5000000 INFO @ Sat, 11 Dec 2021 11:45:37: 10000000 INFO @ Sat, 11 Dec 2021 11:45:37: 1000000 INFO @ Sat, 11 Dec 2021 11:45:43: 6000000 INFO @ Sat, 11 Dec 2021 11:45:44: 11000000 INFO @ Sat, 11 Dec 2021 11:45:45: 2000000 INFO @ Sat, 11 Dec 2021 11:45:50: 7000000 INFO @ Sat, 11 Dec 2021 11:45:51: 12000000 INFO @ Sat, 11 Dec 2021 11:45:52: 3000000 INFO @ Sat, 11 Dec 2021 11:45:58: 8000000 INFO @ Sat, 11 Dec 2021 11:45:58: 13000000 INFO @ Sat, 11 Dec 2021 11:45:59: 4000000 INFO @ Sat, 11 Dec 2021 11:46:05: 9000000 INFO @ Sat, 11 Dec 2021 11:46:05: 14000000 INFO @ Sat, 11 Dec 2021 11:46:07: 5000000 INFO @ Sat, 11 Dec 2021 11:46:12: 10000000 INFO @ Sat, 11 Dec 2021 11:46:13: 15000000 INFO @ Sat, 11 Dec 2021 11:46:14: 6000000 INFO @ Sat, 11 Dec 2021 11:46:19: 11000000 INFO @ Sat, 11 Dec 2021 11:46:20: 16000000 INFO @ Sat, 11 Dec 2021 11:46:21: 7000000 INFO @ Sat, 11 Dec 2021 11:46:26: #1 tag size is determined as 72 bps INFO @ Sat, 11 Dec 2021 11:46:26: #1 tag size = 72 INFO @ Sat, 11 Dec 2021 11:46:26: #1 total tags in treatment: 8280972 INFO @ Sat, 11 Dec 2021 11:46:26: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:46:26: #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 11:46:26: #1 tags after filtering in treatment: 7697420 INFO @ Sat, 11 Dec 2021 11:46:26: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 11 Dec 2021 11:46:26: #1 finished! INFO @ Sat, 11 Dec 2021 11:46:26: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:46:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:46:27: 12000000 INFO @ Sat, 11 Dec 2021 11:46:27: #2 number of paired peaks: 1773 INFO @ Sat, 11 Dec 2021 11:46:27: start model_add_line... INFO @ Sat, 11 Dec 2021 11:46:27: start X-correlation... INFO @ Sat, 11 Dec 2021 11:46:27: end of X-cor INFO @ Sat, 11 Dec 2021 11:46:27: #2 finished! INFO @ Sat, 11 Dec 2021 11:46:27: #2 predicted fragment length is 170 bps INFO @ Sat, 11 Dec 2021 11:46:27: #2 alternative fragment length(s) may be 170 bps INFO @ Sat, 11 Dec 2021 11:46:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005674/SRX9005674.05_model.r INFO @ Sat, 11 Dec 2021 11:46:27: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:46:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:46:29: 8000000 INFO @ Sat, 11 Dec 2021 11:46:34: 13000000 INFO @ Sat, 11 Dec 2021 11:46:36: 9000000 INFO @ Sat, 11 Dec 2021 11:46:41: 14000000 INFO @ Sat, 11 Dec 2021 11:46:43: 10000000 INFO @ Sat, 11 Dec 2021 11:46:44: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:46:48: 15000000 INFO @ Sat, 11 Dec 2021 11:46:50: 11000000 INFO @ Sat, 11 Dec 2021 11:46:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005674/SRX9005674.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:46:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005674/SRX9005674.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:46:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005674/SRX9005674.05_summits.bed INFO @ Sat, 11 Dec 2021 11:46:54: Done! INFO @ Sat, 11 Dec 2021 11:46:55: 16000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4530 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:46:58: 12000000 INFO @ Sat, 11 Dec 2021 11:47:02: #1 tag size is determined as 72 bps INFO @ Sat, 11 Dec 2021 11:47:02: #1 tag size = 72 INFO @ Sat, 11 Dec 2021 11:47:02: #1 total tags in treatment: 8280972 INFO @ Sat, 11 Dec 2021 11:47:02: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:47:02: #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 11:47:02: #1 tags after filtering in treatment: 7697420 INFO @ Sat, 11 Dec 2021 11:47:02: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 11 Dec 2021 11:47:02: #1 finished! INFO @ Sat, 11 Dec 2021 11:47:02: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:47:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:47:02: #2 number of paired peaks: 1773 INFO @ Sat, 11 Dec 2021 11:47:02: start model_add_line... INFO @ Sat, 11 Dec 2021 11:47:03: start X-correlation... INFO @ Sat, 11 Dec 2021 11:47:03: end of X-cor INFO @ Sat, 11 Dec 2021 11:47:03: #2 finished! INFO @ Sat, 11 Dec 2021 11:47:03: #2 predicted fragment length is 170 bps INFO @ Sat, 11 Dec 2021 11:47:03: #2 alternative fragment length(s) may be 170 bps INFO @ Sat, 11 Dec 2021 11:47:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005674/SRX9005674.10_model.r INFO @ Sat, 11 Dec 2021 11:47:03: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:47:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:47:05: 13000000 INFO @ Sat, 11 Dec 2021 11:47:11: 14000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:47:18: 15000000 INFO @ Sat, 11 Dec 2021 11:47:19: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:47:24: 16000000 INFO @ Sat, 11 Dec 2021 11:47:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005674/SRX9005674.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:47:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005674/SRX9005674.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:47:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005674/SRX9005674.10_summits.bed INFO @ Sat, 11 Dec 2021 11:47:28: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2763 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:47:30: #1 tag size is determined as 72 bps INFO @ Sat, 11 Dec 2021 11:47:30: #1 tag size = 72 INFO @ Sat, 11 Dec 2021 11:47:30: #1 total tags in treatment: 8280972 INFO @ Sat, 11 Dec 2021 11:47:30: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:47:30: #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 11:47:30: #1 tags after filtering in treatment: 7697420 INFO @ Sat, 11 Dec 2021 11:47:30: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 11 Dec 2021 11:47:30: #1 finished! INFO @ Sat, 11 Dec 2021 11:47:30: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:47:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:47:31: #2 number of paired peaks: 1773 INFO @ Sat, 11 Dec 2021 11:47:31: start model_add_line... INFO @ Sat, 11 Dec 2021 11:47:31: start X-correlation... INFO @ Sat, 11 Dec 2021 11:47:31: end of X-cor INFO @ Sat, 11 Dec 2021 11:47:31: #2 finished! INFO @ Sat, 11 Dec 2021 11:47:31: #2 predicted fragment length is 170 bps INFO @ Sat, 11 Dec 2021 11:47:31: #2 alternative fragment length(s) may be 170 bps INFO @ Sat, 11 Dec 2021 11:47:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005674/SRX9005674.20_model.r INFO @ Sat, 11 Dec 2021 11:47:31: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:47:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:47:48: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:47:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005674/SRX9005674.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:47:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005674/SRX9005674.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:47:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005674/SRX9005674.20_summits.bed INFO @ Sat, 11 Dec 2021 11:47:56: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1555 records, 4 fields): 4 millis CompletedMACS2peakCalling