Job ID = 14172482 SRX = SRX7628890 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 19737089 spots for SRR10963252/SRR10963252.sra Written 19737089 spots for SRR10963252/SRR10963252.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172988 ("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: 00:18:43 19737089 reads; of these: 19737089 (100.00%) were paired; of these: 9435099 (47.80%) aligned concordantly 0 times 7716171 (39.09%) aligned concordantly exactly 1 time 2585819 (13.10%) aligned concordantly >1 times ---- 9435099 pairs aligned concordantly 0 times; of these: 76368 (0.81%) aligned discordantly 1 time ---- 9358731 pairs aligned 0 times concordantly or discordantly; of these: 18717462 mates make up the pairs; of these: 18156550 (97.00%) aligned 0 times 284221 (1.52%) aligned exactly 1 time 276691 (1.48%) aligned >1 times 54.00% overall alignment rate Time searching: 00:18:43 Overall time: 00:18:43 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 12 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] 801145 / 10374132 = 0.0772 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 15:59:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628890/SRX7628890.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628890/SRX7628890.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628890/SRX7628890.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628890/SRX7628890.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 15:59:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:59:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:59:51: 1000000 INFO @ Sat, 11 Dec 2021 15:59:57: 2000000 INFO @ Sat, 11 Dec 2021 16:00:03: 3000000 INFO @ Sat, 11 Dec 2021 16:00:09: 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 16:00:15: 5000000 INFO @ Sat, 11 Dec 2021 16:00:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628890/SRX7628890.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628890/SRX7628890.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628890/SRX7628890.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628890/SRX7628890.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 16:00:15: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:00:15: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:00:21: 6000000 INFO @ Sat, 11 Dec 2021 16:00:22: 1000000 INFO @ Sat, 11 Dec 2021 16:00:28: 7000000 INFO @ Sat, 11 Dec 2021 16:00:29: 2000000 INFO @ Sat, 11 Dec 2021 16:00:34: 8000000 INFO @ Sat, 11 Dec 2021 16:00:37: 3000000 INFO @ Sat, 11 Dec 2021 16:00:40: 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 16:00:44: 4000000 INFO @ Sat, 11 Dec 2021 16:00:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628890/SRX7628890.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628890/SRX7628890.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628890/SRX7628890.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628890/SRX7628890.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 16:00:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:00:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:00:46: 10000000 INFO @ Sat, 11 Dec 2021 16:00:51: 5000000 INFO @ Sat, 11 Dec 2021 16:00:51: 1000000 INFO @ Sat, 11 Dec 2021 16:00:53: 11000000 INFO @ Sat, 11 Dec 2021 16:00:58: 2000000 INFO @ Sat, 11 Dec 2021 16:00:58: 6000000 INFO @ Sat, 11 Dec 2021 16:00:59: 12000000 INFO @ Sat, 11 Dec 2021 16:01:04: 3000000 INFO @ Sat, 11 Dec 2021 16:01:05: 13000000 INFO @ Sat, 11 Dec 2021 16:01:06: 7000000 INFO @ Sat, 11 Dec 2021 16:01:11: 4000000 INFO @ Sat, 11 Dec 2021 16:01:12: 14000000 INFO @ Sat, 11 Dec 2021 16:01:13: 8000000 INFO @ Sat, 11 Dec 2021 16:01:17: 5000000 INFO @ Sat, 11 Dec 2021 16:01:18: 15000000 INFO @ Sat, 11 Dec 2021 16:01:19: 9000000 INFO @ Sat, 11 Dec 2021 16:01:23: 6000000 INFO @ Sat, 11 Dec 2021 16:01:25: 16000000 INFO @ Sat, 11 Dec 2021 16:01:25: 10000000 INFO @ Sat, 11 Dec 2021 16:01:30: 7000000 INFO @ Sat, 11 Dec 2021 16:01:31: 17000000 INFO @ Sat, 11 Dec 2021 16:01:32: 11000000 INFO @ Sat, 11 Dec 2021 16:01:36: 8000000 INFO @ Sat, 11 Dec 2021 16:01:38: 12000000 INFO @ Sat, 11 Dec 2021 16:01:39: 18000000 INFO @ Sat, 11 Dec 2021 16:01:44: 9000000 INFO @ Sat, 11 Dec 2021 16:01:44: 13000000 INFO @ Sat, 11 Dec 2021 16:01:46: 19000000 INFO @ Sat, 11 Dec 2021 16:01:50: 14000000 INFO @ Sat, 11 Dec 2021 16:01:51: 10000000 INFO @ Sat, 11 Dec 2021 16:01:51: #1 tag size is determined as 43 bps INFO @ Sat, 11 Dec 2021 16:01:51: #1 tag size = 43 INFO @ Sat, 11 Dec 2021 16:01:51: #1 total tags in treatment: 9504604 INFO @ Sat, 11 Dec 2021 16:01:51: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:01:51: #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 16:01:51: #1 tags after filtering in treatment: 8400307 INFO @ Sat, 11 Dec 2021 16:01:51: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 11 Dec 2021 16:01:51: #1 finished! INFO @ Sat, 11 Dec 2021 16:01:51: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:01:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:01:52: #2 number of paired peaks: 5370 INFO @ Sat, 11 Dec 2021 16:01:52: start model_add_line... INFO @ Sat, 11 Dec 2021 16:01:52: start X-correlation... INFO @ Sat, 11 Dec 2021 16:01:52: end of X-cor INFO @ Sat, 11 Dec 2021 16:01:52: #2 finished! INFO @ Sat, 11 Dec 2021 16:01:52: #2 predicted fragment length is 174 bps INFO @ Sat, 11 Dec 2021 16:01:52: #2 alternative fragment length(s) may be 174 bps INFO @ Sat, 11 Dec 2021 16:01:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628890/SRX7628890.05_model.r INFO @ Sat, 11 Dec 2021 16:01:52: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:01:52: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 16:01:57: 15000000 INFO @ Sat, 11 Dec 2021 16:01:58: 11000000 INFO @ Sat, 11 Dec 2021 16:02:03: 16000000 INFO @ Sat, 11 Dec 2021 16:02:05: 12000000 INFO @ Sat, 11 Dec 2021 16:02:10: 17000000 INFO @ Sat, 11 Dec 2021 16:02:13: 13000000 INFO @ Sat, 11 Dec 2021 16:02:15: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:02:18: 18000000 INFO @ Sat, 11 Dec 2021 16:02:21: 14000000 INFO @ Sat, 11 Dec 2021 16:02:27: 19000000 INFO @ Sat, 11 Dec 2021 16:02:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628890/SRX7628890.05_peaks.xls BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 16:02:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628890/SRX7628890.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:02:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628890/SRX7628890.05_summits.bed INFO @ Sat, 11 Dec 2021 16:02:28: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7943 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:02:30: 15000000 INFO @ Sat, 11 Dec 2021 16:02:33: #1 tag size is determined as 43 bps INFO @ Sat, 11 Dec 2021 16:02:33: #1 tag size = 43 INFO @ Sat, 11 Dec 2021 16:02:33: #1 total tags in treatment: 9504604 INFO @ Sat, 11 Dec 2021 16:02:33: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:02:33: #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 16:02:33: #1 tags after filtering in treatment: 8400307 INFO @ Sat, 11 Dec 2021 16:02:33: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 11 Dec 2021 16:02:33: #1 finished! INFO @ Sat, 11 Dec 2021 16:02:33: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:02:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:02:34: #2 number of paired peaks: 5370 INFO @ Sat, 11 Dec 2021 16:02:34: start model_add_line... INFO @ Sat, 11 Dec 2021 16:02:34: start X-correlation... INFO @ Sat, 11 Dec 2021 16:02:34: end of X-cor INFO @ Sat, 11 Dec 2021 16:02:34: #2 finished! INFO @ Sat, 11 Dec 2021 16:02:34: #2 predicted fragment length is 174 bps INFO @ Sat, 11 Dec 2021 16:02:34: #2 alternative fragment length(s) may be 174 bps INFO @ Sat, 11 Dec 2021 16:02:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628890/SRX7628890.10_model.r INFO @ Sat, 11 Dec 2021 16:02:34: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:02:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:02:38: 16000000 INFO @ Sat, 11 Dec 2021 16:02:45: 17000000 INFO @ Sat, 11 Dec 2021 16:02:51: 18000000 INFO @ Sat, 11 Dec 2021 16:02:57: 19000000 INFO @ Sat, 11 Dec 2021 16:03:00: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:03:02: #1 tag size is determined as 43 bps INFO @ Sat, 11 Dec 2021 16:03:02: #1 tag size = 43 INFO @ Sat, 11 Dec 2021 16:03:02: #1 total tags in treatment: 9504604 INFO @ Sat, 11 Dec 2021 16:03:02: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:03:02: #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 16:03:02: #1 tags after filtering in treatment: 8400307 INFO @ Sat, 11 Dec 2021 16:03:02: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 11 Dec 2021 16:03:02: #1 finished! INFO @ Sat, 11 Dec 2021 16:03:02: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:03:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:03:03: #2 number of paired peaks: 5370 INFO @ Sat, 11 Dec 2021 16:03:03: start model_add_line... INFO @ Sat, 11 Dec 2021 16:03:03: start X-correlation... INFO @ Sat, 11 Dec 2021 16:03:03: end of X-cor INFO @ Sat, 11 Dec 2021 16:03:03: #2 finished! INFO @ Sat, 11 Dec 2021 16:03:03: #2 predicted fragment length is 174 bps INFO @ Sat, 11 Dec 2021 16:03:03: #2 alternative fragment length(s) may be 174 bps INFO @ Sat, 11 Dec 2021 16:03:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628890/SRX7628890.20_model.r INFO @ Sat, 11 Dec 2021 16:03:03: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:03:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:03:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628890/SRX7628890.10_peaks.xls INFO @ Sat, 11 Dec 2021 16:03:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628890/SRX7628890.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:03:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628890/SRX7628890.10_summits.bed INFO @ Sat, 11 Dec 2021 16:03:13: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5142 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:03:28: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:03:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628890/SRX7628890.20_peaks.xls INFO @ Sat, 11 Dec 2021 16:03:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628890/SRX7628890.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:03:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628890/SRX7628890.20_summits.bed INFO @ Sat, 11 Dec 2021 16:03:40: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2702 records, 4 fields): 5 millis CompletedMACS2peakCalling