Job ID = 14167379 SRX = ERX3978902 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18120220 spots for ERR3975971/ERR3975971.sra Written 18120220 spots for ERR3975971/ERR3975971.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168186 ("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: 00:51:48 18120220 reads; of these: 18120220 (100.00%) were paired; of these: 2457532 (13.56%) aligned concordantly 0 times 11960639 (66.01%) aligned concordantly exactly 1 time 3702049 (20.43%) aligned concordantly >1 times ---- 2457532 pairs aligned concordantly 0 times; of these: 618921 (25.18%) aligned discordantly 1 time ---- 1838611 pairs aligned 0 times concordantly or discordantly; of these: 3677222 mates make up the pairs; of these: 1765888 (48.02%) aligned 0 times 820516 (22.31%) aligned exactly 1 time 1090818 (29.66%) aligned >1 times 95.13% overall alignment rate Time searching: 00:51:49 Overall time: 00:51:49 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 16 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] 12611495 / 16229624 = 0.7771 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 13:05:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978902/ERX3978902.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978902/ERX3978902.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978902/ERX3978902.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978902/ERX3978902.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 13:05:06: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:05:06: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:05:12: 1000000 INFO @ Fri, 10 Dec 2021 13:05:17: 2000000 INFO @ Fri, 10 Dec 2021 13:05:22: 3000000 INFO @ Fri, 10 Dec 2021 13:05:28: 4000000 INFO @ Fri, 10 Dec 2021 13:05:33: 5000000 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 13:05:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978902/ERX3978902.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978902/ERX3978902.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978902/ERX3978902.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978902/ERX3978902.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 13:05:36: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:05:36: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:05:39: 6000000 INFO @ Fri, 10 Dec 2021 13:05:42: 1000000 INFO @ Fri, 10 Dec 2021 13:05:45: 7000000 INFO @ Fri, 10 Dec 2021 13:05:48: 2000000 INFO @ Fri, 10 Dec 2021 13:05:51: 8000000 INFO @ Fri, 10 Dec 2021 13:05:54: 3000000 INFO @ Fri, 10 Dec 2021 13:05:57: 9000000 INFO @ Fri, 10 Dec 2021 13:05:58: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 13:05:58: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 13:05:58: #1 total tags in treatment: 3439662 INFO @ Fri, 10 Dec 2021 13:05:58: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:05:58: #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 13:05:58: #1 tags after filtering in treatment: 3060940 INFO @ Fri, 10 Dec 2021 13:05:58: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 10 Dec 2021 13:05:58: #1 finished! INFO @ Fri, 10 Dec 2021 13:05:58: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:05:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:05:59: #2 number of paired peaks: 4891 INFO @ Fri, 10 Dec 2021 13:05:59: start model_add_line... INFO @ Fri, 10 Dec 2021 13:05:59: start X-correlation... INFO @ Fri, 10 Dec 2021 13:05:59: end of X-cor INFO @ Fri, 10 Dec 2021 13:05:59: #2 finished! INFO @ Fri, 10 Dec 2021 13:05:59: #2 predicted fragment length is 207 bps INFO @ Fri, 10 Dec 2021 13:05:59: #2 alternative fragment length(s) may be 207 bps INFO @ Fri, 10 Dec 2021 13:05:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978902/ERX3978902.05_model.r INFO @ Fri, 10 Dec 2021 13:05:59: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:05:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:06:00: 4000000 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 13:06:05: 5000000 INFO @ Fri, 10 Dec 2021 13:06:06: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:06:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978902/ERX3978902.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978902/ERX3978902.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978902/ERX3978902.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978902/ERX3978902.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 13:06:07: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:06:07: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:06:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978902/ERX3978902.05_peaks.xls INFO @ Fri, 10 Dec 2021 13:06:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978902/ERX3978902.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:06:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978902/ERX3978902.05_summits.bed INFO @ Fri, 10 Dec 2021 13:06:10: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8559 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:06:12: 6000000 INFO @ Fri, 10 Dec 2021 13:06:14: 1000000 INFO @ Fri, 10 Dec 2021 13:06:18: 7000000 INFO @ Fri, 10 Dec 2021 13:06:20: 2000000 INFO @ Fri, 10 Dec 2021 13:06:24: 8000000 INFO @ Fri, 10 Dec 2021 13:06:26: 3000000 INFO @ Fri, 10 Dec 2021 13:06:30: 9000000 INFO @ Fri, 10 Dec 2021 13:06:32: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 13:06:32: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 13:06:32: #1 total tags in treatment: 3439662 INFO @ Fri, 10 Dec 2021 13:06:32: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:06:32: #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 13:06:32: #1 tags after filtering in treatment: 3060940 INFO @ Fri, 10 Dec 2021 13:06:32: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 10 Dec 2021 13:06:32: #1 finished! INFO @ Fri, 10 Dec 2021 13:06:32: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:06:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:06:32: #2 number of paired peaks: 4891 INFO @ Fri, 10 Dec 2021 13:06:32: start model_add_line... INFO @ Fri, 10 Dec 2021 13:06:32: start X-correlation... INFO @ Fri, 10 Dec 2021 13:06:32: end of X-cor INFO @ Fri, 10 Dec 2021 13:06:32: #2 finished! INFO @ Fri, 10 Dec 2021 13:06:32: #2 predicted fragment length is 207 bps INFO @ Fri, 10 Dec 2021 13:06:32: #2 alternative fragment length(s) may be 207 bps INFO @ Fri, 10 Dec 2021 13:06:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978902/ERX3978902.10_model.r INFO @ Fri, 10 Dec 2021 13:06:32: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:06:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:06:32: 4000000 INFO @ Fri, 10 Dec 2021 13:06:38: 5000000 INFO @ Fri, 10 Dec 2021 13:06:39: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:06:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978902/ERX3978902.10_peaks.xls INFO @ Fri, 10 Dec 2021 13:06:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978902/ERX3978902.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:06:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978902/ERX3978902.10_summits.bed INFO @ Fri, 10 Dec 2021 13:06:43: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5305 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:06:44: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 13:06:50: 7000000 INFO @ Fri, 10 Dec 2021 13:06:55: 8000000 INFO @ Fri, 10 Dec 2021 13:07:01: 9000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 13:07:02: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 13:07:02: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 13:07:02: #1 total tags in treatment: 3439662 INFO @ Fri, 10 Dec 2021 13:07:02: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:07:02: #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 13:07:02: #1 tags after filtering in treatment: 3060940 INFO @ Fri, 10 Dec 2021 13:07:02: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 10 Dec 2021 13:07:02: #1 finished! INFO @ Fri, 10 Dec 2021 13:07:02: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:07:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:07:03: #2 number of paired peaks: 4891 INFO @ Fri, 10 Dec 2021 13:07:03: start model_add_line... INFO @ Fri, 10 Dec 2021 13:07:03: start X-correlation... INFO @ Fri, 10 Dec 2021 13:07:03: end of X-cor INFO @ Fri, 10 Dec 2021 13:07:03: #2 finished! INFO @ Fri, 10 Dec 2021 13:07:03: #2 predicted fragment length is 207 bps INFO @ Fri, 10 Dec 2021 13:07:03: #2 alternative fragment length(s) may be 207 bps INFO @ Fri, 10 Dec 2021 13:07:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978902/ERX3978902.20_model.r INFO @ Fri, 10 Dec 2021 13:07:03: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:07:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:07:10: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:07:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978902/ERX3978902.20_peaks.xls INFO @ Fri, 10 Dec 2021 13:07:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978902/ERX3978902.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:07:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978902/ERX3978902.20_summits.bed INFO @ Fri, 10 Dec 2021 13:07:14: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2202 records, 4 fields): 3 millis CompletedMACS2peakCalling