Job ID = 14168657 SRX = ERX3978870 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 31653804 spots for ERR3975939/ERR3975939.sra Written 31653804 spots for ERR3975939/ERR3975939.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169866 ("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: 01:29:00 31653804 reads; of these: 31653804 (100.00%) were paired; of these: 4211242 (13.30%) aligned concordantly 0 times 22507323 (71.10%) aligned concordantly exactly 1 time 4935239 (15.59%) aligned concordantly >1 times ---- 4211242 pairs aligned concordantly 0 times; of these: 937279 (22.26%) aligned discordantly 1 time ---- 3273963 pairs aligned 0 times concordantly or discordantly; of these: 6547926 mates make up the pairs; of these: 3286252 (50.19%) aligned 0 times 1765205 (26.96%) aligned exactly 1 time 1496469 (22.85%) aligned >1 times 94.81% overall alignment rate Time searching: 01:29:00 Overall time: 01:29:00 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 28 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] 19808404 / 28217302 = 0.7020 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 20:54:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978870/ERX3978870.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978870/ERX3978870.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978870/ERX3978870.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978870/ERX3978870.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 20:54:06: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:54:06: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:54:14: 1000000 INFO @ Fri, 10 Dec 2021 20:54:22: 2000000 INFO @ Fri, 10 Dec 2021 20:54:30: 3000000 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 20:54:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978870/ERX3978870.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978870/ERX3978870.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978870/ERX3978870.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978870/ERX3978870.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 20:54:36: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:54:36: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:54:38: 4000000 INFO @ Fri, 10 Dec 2021 20:54:42: 1000000 INFO @ Fri, 10 Dec 2021 20:54:46: 5000000 INFO @ Fri, 10 Dec 2021 20:54:48: 2000000 INFO @ Fri, 10 Dec 2021 20:54:54: 3000000 INFO @ Fri, 10 Dec 2021 20:54:55: 6000000 INFO @ Fri, 10 Dec 2021 20:55:01: 4000000 INFO @ Fri, 10 Dec 2021 20:55:03: 7000000 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 20:55:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978870/ERX3978870.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978870/ERX3978870.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978870/ERX3978870.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978870/ERX3978870.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 20:55:06: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:55:06: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:55:07: 5000000 INFO @ Fri, 10 Dec 2021 20:55:12: 8000000 INFO @ Fri, 10 Dec 2021 20:55:13: 6000000 INFO @ Fri, 10 Dec 2021 20:55:15: 1000000 INFO @ Fri, 10 Dec 2021 20:55:20: 7000000 INFO @ Fri, 10 Dec 2021 20:55:20: 9000000 INFO @ Fri, 10 Dec 2021 20:55:23: 2000000 INFO @ Fri, 10 Dec 2021 20:55:26: 8000000 INFO @ Fri, 10 Dec 2021 20:55:29: 10000000 INFO @ Fri, 10 Dec 2021 20:55:31: 3000000 INFO @ Fri, 10 Dec 2021 20:55:32: 9000000 INFO @ Fri, 10 Dec 2021 20:55:38: 11000000 INFO @ Fri, 10 Dec 2021 20:55:39: 10000000 INFO @ Fri, 10 Dec 2021 20:55:39: 4000000 INFO @ Fri, 10 Dec 2021 20:55:45: 11000000 INFO @ Fri, 10 Dec 2021 20:55:46: 12000000 INFO @ Fri, 10 Dec 2021 20:55:47: 5000000 INFO @ Fri, 10 Dec 2021 20:55:51: 12000000 INFO @ Fri, 10 Dec 2021 20:55:55: 13000000 INFO @ Fri, 10 Dec 2021 20:55:56: 6000000 INFO @ Fri, 10 Dec 2021 20:55:58: 13000000 INFO @ Fri, 10 Dec 2021 20:56:03: 14000000 INFO @ Fri, 10 Dec 2021 20:56:04: 7000000 INFO @ Fri, 10 Dec 2021 20:56:04: 14000000 INFO @ Fri, 10 Dec 2021 20:56:12: 15000000 INFO @ Fri, 10 Dec 2021 20:56:12: 15000000 INFO @ Fri, 10 Dec 2021 20:56:12: 8000000 INFO @ Fri, 10 Dec 2021 20:56:19: 16000000 INFO @ Fri, 10 Dec 2021 20:56:20: 9000000 INFO @ Fri, 10 Dec 2021 20:56:21: 16000000 INFO @ Fri, 10 Dec 2021 20:56:26: 17000000 INFO @ Fri, 10 Dec 2021 20:56:28: 10000000 INFO @ Fri, 10 Dec 2021 20:56:30: 17000000 INFO @ Fri, 10 Dec 2021 20:56:32: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 20:56:37: 11000000 INFO @ Fri, 10 Dec 2021 20:56:39: 19000000 INFO @ Fri, 10 Dec 2021 20:56:39: 18000000 INFO @ Fri, 10 Dec 2021 20:56:45: 12000000 INFO @ Fri, 10 Dec 2021 20:56:45: 20000000 INFO @ Fri, 10 Dec 2021 20:56:47: 19000000 INFO @ Fri, 10 Dec 2021 20:56:48: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 20:56:48: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 20:56:48: #1 total tags in treatment: 8232066 INFO @ Fri, 10 Dec 2021 20:56:48: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:56:48: #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 20:56:48: #1 tags after filtering in treatment: 7129761 INFO @ Fri, 10 Dec 2021 20:56:48: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 10 Dec 2021 20:56:48: #1 finished! INFO @ Fri, 10 Dec 2021 20:56:48: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:56:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:56:49: #2 number of paired peaks: 6265 INFO @ Fri, 10 Dec 2021 20:56:49: start model_add_line... INFO @ Fri, 10 Dec 2021 20:56:49: start X-correlation... INFO @ Fri, 10 Dec 2021 20:56:49: end of X-cor INFO @ Fri, 10 Dec 2021 20:56:49: #2 finished! INFO @ Fri, 10 Dec 2021 20:56:49: #2 predicted fragment length is 175 bps INFO @ Fri, 10 Dec 2021 20:56:49: #2 alternative fragment length(s) may be 175 bps INFO @ Fri, 10 Dec 2021 20:56:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978870/ERX3978870.10_model.r INFO @ Fri, 10 Dec 2021 20:56:49: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:56:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:56:53: 13000000 INFO @ Fri, 10 Dec 2021 20:56:56: 20000000 INFO @ Fri, 10 Dec 2021 20:56:59: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 20:56:59: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 20:56:59: #1 total tags in treatment: 8232066 INFO @ Fri, 10 Dec 2021 20:56:59: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:56:59: #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 20:56:59: #1 tags after filtering in treatment: 7129761 INFO @ Fri, 10 Dec 2021 20:56:59: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 10 Dec 2021 20:56:59: #1 finished! INFO @ Fri, 10 Dec 2021 20:56:59: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:56:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:57:00: #2 number of paired peaks: 6265 INFO @ Fri, 10 Dec 2021 20:57:00: start model_add_line... INFO @ Fri, 10 Dec 2021 20:57:00: start X-correlation... INFO @ Fri, 10 Dec 2021 20:57:00: end of X-cor INFO @ Fri, 10 Dec 2021 20:57:00: #2 finished! INFO @ Fri, 10 Dec 2021 20:57:00: #2 predicted fragment length is 175 bps INFO @ Fri, 10 Dec 2021 20:57:00: #2 alternative fragment length(s) may be 175 bps INFO @ Fri, 10 Dec 2021 20:57:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978870/ERX3978870.05_model.r INFO @ Fri, 10 Dec 2021 20:57:00: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:57:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:57:01: 14000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 20:57:06: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:57:09: 15000000 INFO @ Fri, 10 Dec 2021 20:57:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978870/ERX3978870.10_peaks.xls INFO @ Fri, 10 Dec 2021 20:57:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978870/ERX3978870.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:57:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978870/ERX3978870.10_summits.bed INFO @ Fri, 10 Dec 2021 20:57:14: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6971 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 20:57:17: 16000000 INFO @ Fri, 10 Dec 2021 20:57:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:57:25: 17000000 INFO @ Fri, 10 Dec 2021 20:57:31: 18000000 INFO @ Fri, 10 Dec 2021 20:57:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978870/ERX3978870.05_peaks.xls INFO @ Fri, 10 Dec 2021 20:57:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978870/ERX3978870.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:57:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978870/ERX3978870.05_summits.bed INFO @ Fri, 10 Dec 2021 20:57:34: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9492 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 20:57:37: 19000000 INFO @ Fri, 10 Dec 2021 20:57:42: 20000000 INFO @ Fri, 10 Dec 2021 20:57:44: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 20:57:44: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 20:57:44: #1 total tags in treatment: 8232066 INFO @ Fri, 10 Dec 2021 20:57:44: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:57:44: #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 20:57:44: #1 tags after filtering in treatment: 7129761 INFO @ Fri, 10 Dec 2021 20:57:44: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 10 Dec 2021 20:57:44: #1 finished! INFO @ Fri, 10 Dec 2021 20:57:44: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:57:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:57:45: #2 number of paired peaks: 6265 INFO @ Fri, 10 Dec 2021 20:57:45: start model_add_line... INFO @ Fri, 10 Dec 2021 20:57:45: start X-correlation... INFO @ Fri, 10 Dec 2021 20:57:45: end of X-cor INFO @ Fri, 10 Dec 2021 20:57:45: #2 finished! INFO @ Fri, 10 Dec 2021 20:57:45: #2 predicted fragment length is 175 bps INFO @ Fri, 10 Dec 2021 20:57:45: #2 alternative fragment length(s) may be 175 bps INFO @ Fri, 10 Dec 2021 20:57:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978870/ERX3978870.20_model.r INFO @ Fri, 10 Dec 2021 20:57:45: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:57:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:58:02: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:58:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978870/ERX3978870.20_peaks.xls INFO @ Fri, 10 Dec 2021 20:58:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978870/ERX3978870.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:58:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978870/ERX3978870.20_summits.bed INFO @ Fri, 10 Dec 2021 20:58:10: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5498 records, 4 fields): 8 millis CompletedMACS2peakCalling