Job ID = 16437589 SRX = ERX5847880 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T03:51:16 prefetch.2.10.7: 1) Downloading 'ERR6212890'... 2022-08-02T03:51:16 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T03:51:42 prefetch.2.10.7: HTTPS download succeed 2022-08-02T03:51:43 prefetch.2.10.7: 'ERR6212890' is valid 2022-08-02T03:51:43 prefetch.2.10.7: 1) 'ERR6212890' was downloaded successfully 2022-08-02T03:51:43 prefetch.2.10.7: 'ERR6212890' has 0 unresolved dependencies Read 7202825 spots for ERR6212890/ERR6212890.sra Written 7202825 spots for ERR6212890/ERR6212890.sra fastq に変換しました。 bowtie でマッピング中... Your job 16437782 ("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: 00:06:55 7202825 reads; of these: 7202825 (100.00%) were paired; of these: 2501400 (34.73%) aligned concordantly 0 times 4014701 (55.74%) aligned concordantly exactly 1 time 686724 (9.53%) aligned concordantly >1 times ---- 2501400 pairs aligned concordantly 0 times; of these: 13227 (0.53%) aligned discordantly 1 time ---- 2488173 pairs aligned 0 times concordantly or discordantly; of these: 4976346 mates make up the pairs; of these: 4314552 (86.70%) aligned 0 times 550125 (11.05%) aligned exactly 1 time 111669 (2.24%) aligned >1 times 70.05% overall alignment rate Time searching: 00:06:55 Overall time: 00:06:55 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] 156706 / 4712613 = 0.0333 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:04:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX5847880/ERX5847880.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX5847880/ERX5847880.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX5847880/ERX5847880.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX5847880/ERX5847880.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 @ Tue, 02 Aug 2022 13:04:56: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:04:56: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:05:06: 1000000 INFO @ Tue, 02 Aug 2022 13:05:16: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:05:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX5847880/ERX5847880.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX5847880/ERX5847880.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX5847880/ERX5847880.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX5847880/ERX5847880.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 @ Tue, 02 Aug 2022 13:05:24: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:05:24: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:05:24: 3000000 INFO @ Tue, 02 Aug 2022 13:05:34: 4000000 INFO @ Tue, 02 Aug 2022 13:05:35: 1000000 INFO @ Tue, 02 Aug 2022 13:05:43: 5000000 INFO @ Tue, 02 Aug 2022 13:05:46: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:05:53: 6000000 INFO @ Tue, 02 Aug 2022 13:05:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX5847880/ERX5847880.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX5847880/ERX5847880.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX5847880/ERX5847880.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX5847880/ERX5847880.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 @ Tue, 02 Aug 2022 13:05:54: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:05:54: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:05:57: 3000000 INFO @ Tue, 02 Aug 2022 13:06:02: 7000000 INFO @ Tue, 02 Aug 2022 13:06:04: 1000000 INFO @ Tue, 02 Aug 2022 13:06:07: 4000000 INFO @ Tue, 02 Aug 2022 13:06:12: 8000000 INFO @ Tue, 02 Aug 2022 13:06:14: 2000000 INFO @ Tue, 02 Aug 2022 13:06:19: 5000000 INFO @ Tue, 02 Aug 2022 13:06:21: 9000000 INFO @ Tue, 02 Aug 2022 13:06:24: 3000000 INFO @ Tue, 02 Aug 2022 13:06:29: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 13:06:29: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 13:06:29: #1 total tags in treatment: 4544770 INFO @ Tue, 02 Aug 2022 13:06:29: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:06:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:06:29: #1 tags after filtering in treatment: 4434145 INFO @ Tue, 02 Aug 2022 13:06:29: #1 Redundant rate of treatment: 0.02 INFO @ Tue, 02 Aug 2022 13:06:29: #1 finished! INFO @ Tue, 02 Aug 2022 13:06:29: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:06:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:06:29: #2 number of paired peaks: 1519 INFO @ Tue, 02 Aug 2022 13:06:29: start model_add_line... INFO @ Tue, 02 Aug 2022 13:06:29: start X-correlation... INFO @ Tue, 02 Aug 2022 13:06:30: end of X-cor INFO @ Tue, 02 Aug 2022 13:06:30: #2 finished! INFO @ Tue, 02 Aug 2022 13:06:30: #2 predicted fragment length is 144 bps INFO @ Tue, 02 Aug 2022 13:06:30: #2 alternative fragment length(s) may be 144 bps INFO @ Tue, 02 Aug 2022 13:06:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX5847880/ERX5847880.05_model.r INFO @ Tue, 02 Aug 2022 13:06:30: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:06:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:06:30: 6000000 INFO @ Tue, 02 Aug 2022 13:06:34: 4000000 INFO @ Tue, 02 Aug 2022 13:06:41: 7000000 INFO @ Tue, 02 Aug 2022 13:06:43: 5000000 INFO @ Tue, 02 Aug 2022 13:06:44: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:06:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX5847880/ERX5847880.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:06:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX5847880/ERX5847880.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:06:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX5847880/ERX5847880.05_summits.bed INFO @ Tue, 02 Aug 2022 13:06:51: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (594 records, 4 fields): 56 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:06:52: 8000000 INFO @ Tue, 02 Aug 2022 13:06:53: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:07:03: 7000000 INFO @ Tue, 02 Aug 2022 13:07:04: 9000000 INFO @ Tue, 02 Aug 2022 13:07:12: 8000000 INFO @ Tue, 02 Aug 2022 13:07:13: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 13:07:13: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 13:07:13: #1 total tags in treatment: 4544770 INFO @ Tue, 02 Aug 2022 13:07:13: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:07:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:07:13: #1 tags after filtering in treatment: 4434145 INFO @ Tue, 02 Aug 2022 13:07:13: #1 Redundant rate of treatment: 0.02 INFO @ Tue, 02 Aug 2022 13:07:13: #1 finished! INFO @ Tue, 02 Aug 2022 13:07:13: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:07:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:07:14: #2 number of paired peaks: 1519 INFO @ Tue, 02 Aug 2022 13:07:14: start model_add_line... INFO @ Tue, 02 Aug 2022 13:07:14: start X-correlation... INFO @ Tue, 02 Aug 2022 13:07:14: end of X-cor INFO @ Tue, 02 Aug 2022 13:07:14: #2 finished! INFO @ Tue, 02 Aug 2022 13:07:14: #2 predicted fragment length is 144 bps INFO @ Tue, 02 Aug 2022 13:07:14: #2 alternative fragment length(s) may be 144 bps INFO @ Tue, 02 Aug 2022 13:07:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX5847880/ERX5847880.10_model.r INFO @ Tue, 02 Aug 2022 13:07:14: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:07:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:07:22: 9000000 INFO @ Tue, 02 Aug 2022 13:07:28: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:07:29: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 13:07:29: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 13:07:29: #1 total tags in treatment: 4544770 INFO @ Tue, 02 Aug 2022 13:07:29: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:07:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:07:29: #1 tags after filtering in treatment: 4434145 INFO @ Tue, 02 Aug 2022 13:07:29: #1 Redundant rate of treatment: 0.02 INFO @ Tue, 02 Aug 2022 13:07:29: #1 finished! INFO @ Tue, 02 Aug 2022 13:07:29: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:07:29: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:07:30: #2 number of paired peaks: 1519 INFO @ Tue, 02 Aug 2022 13:07:30: start model_add_line... INFO @ Tue, 02 Aug 2022 13:07:30: start X-correlation... INFO @ Tue, 02 Aug 2022 13:07:30: end of X-cor INFO @ Tue, 02 Aug 2022 13:07:30: #2 finished! INFO @ Tue, 02 Aug 2022 13:07:30: #2 predicted fragment length is 144 bps INFO @ Tue, 02 Aug 2022 13:07:30: #2 alternative fragment length(s) may be 144 bps INFO @ Tue, 02 Aug 2022 13:07:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX5847880/ERX5847880.20_model.r INFO @ Tue, 02 Aug 2022 13:07:30: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:07:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:07:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX5847880/ERX5847880.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:07:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX5847880/ERX5847880.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:07:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX5847880/ERX5847880.10_summits.bed INFO @ Tue, 02 Aug 2022 13:07:36: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (198 records, 4 fields): 127 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:07:44: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:07:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX5847880/ERX5847880.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:07:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX5847880/ERX5847880.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:07:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX5847880/ERX5847880.20_summits.bed INFO @ Tue, 02 Aug 2022 13:07:51: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (89 records, 4 fields): 16 millis CompletedMACS2peakCalling