Job ID = 16436936 SRX = SRX11638461 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T03:07:08 prefetch.2.10.7: 1) Downloading 'SRR15334170'... 2022-08-02T03:07:08 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T03:07:15 prefetch.2.10.7: HTTPS download succeed 2022-08-02T03:07:16 prefetch.2.10.7: 'SRR15334170' is valid 2022-08-02T03:07:16 prefetch.2.10.7: 1) 'SRR15334170' was downloaded successfully 2022-08-02T03:07:16 prefetch.2.10.7: 'SRR15334170' has 0 unresolved dependencies Read 15036020 spots for SRR15334170/SRR15334170.sra Written 15036020 spots for SRR15334170/SRR15334170.sra fastq に変換しました。 bowtie でマッピング中... Your job 16437137 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:03:11 15036020 reads; of these: 15036020 (100.00%) were unpaired; of these: 1615546 (10.74%) aligned 0 times 12347971 (82.12%) aligned exactly 1 time 1072503 (7.13%) aligned >1 times 89.26% overall alignment rate Time searching: 00:03:12 Overall time: 00:03:12 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_rmdupse_core] 3571378 / 13420474 = 0.2661 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 12:14:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11638461/SRX11638461.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11638461/SRX11638461.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11638461/SRX11638461.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11638461/SRX11638461.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 12:14:09: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:14:09: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:14:15: 1000000 INFO @ Tue, 02 Aug 2022 12:14:21: 2000000 INFO @ Tue, 02 Aug 2022 12:14:26: 3000000 INFO @ Tue, 02 Aug 2022 12:14:31: 4000000 INFO @ Tue, 02 Aug 2022 12:14:36: 5000000 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 12:14:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11638461/SRX11638461.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11638461/SRX11638461.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11638461/SRX11638461.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11638461/SRX11638461.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 12:14:39: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:14:39: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:14:41: 6000000 INFO @ Tue, 02 Aug 2022 12:14:45: 1000000 INFO @ Tue, 02 Aug 2022 12:14:46: 7000000 INFO @ Tue, 02 Aug 2022 12:14:50: 2000000 INFO @ Tue, 02 Aug 2022 12:14:52: 8000000 INFO @ Tue, 02 Aug 2022 12:14:55: 3000000 INFO @ Tue, 02 Aug 2022 12:14:57: 9000000 INFO @ Tue, 02 Aug 2022 12:15:01: 4000000 INFO @ Tue, 02 Aug 2022 12:15:02: #1 tag size is determined as 49 bps INFO @ Tue, 02 Aug 2022 12:15:02: #1 tag size = 49 INFO @ Tue, 02 Aug 2022 12:15:02: #1 total tags in treatment: 9849096 INFO @ Tue, 02 Aug 2022 12:15:02: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:15:02: #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 12:15:02: #1 tags after filtering in treatment: 9849096 INFO @ Tue, 02 Aug 2022 12:15:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:15:02: #1 finished! INFO @ Tue, 02 Aug 2022 12:15:02: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:15:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:15:02: #2 number of paired peaks: 1720 INFO @ Tue, 02 Aug 2022 12:15:02: start model_add_line... INFO @ Tue, 02 Aug 2022 12:15:03: start X-correlation... INFO @ Tue, 02 Aug 2022 12:15:03: end of X-cor INFO @ Tue, 02 Aug 2022 12:15:03: #2 finished! INFO @ Tue, 02 Aug 2022 12:15:03: #2 predicted fragment length is 296 bps INFO @ Tue, 02 Aug 2022 12:15:03: #2 alternative fragment length(s) may be 296 bps INFO @ Tue, 02 Aug 2022 12:15:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11638461/SRX11638461.05_model.r INFO @ Tue, 02 Aug 2022 12:15:03: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:15:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:15:06: 5000000 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 12:15:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11638461/SRX11638461.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11638461/SRX11638461.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11638461/SRX11638461.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11638461/SRX11638461.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 12:15:09: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:15:09: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:15:11: 6000000 INFO @ Tue, 02 Aug 2022 12:15:15: 1000000 INFO @ Tue, 02 Aug 2022 12:15:16: 7000000 INFO @ Tue, 02 Aug 2022 12:15:20: 2000000 INFO @ Tue, 02 Aug 2022 12:15:21: 8000000 INFO @ Tue, 02 Aug 2022 12:15:25: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:15:26: 3000000 INFO @ Tue, 02 Aug 2022 12:15:27: 9000000 INFO @ Tue, 02 Aug 2022 12:15:31: 4000000 INFO @ Tue, 02 Aug 2022 12:15:31: #1 tag size is determined as 49 bps INFO @ Tue, 02 Aug 2022 12:15:31: #1 tag size = 49 INFO @ Tue, 02 Aug 2022 12:15:31: #1 total tags in treatment: 9849096 INFO @ Tue, 02 Aug 2022 12:15:31: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:15:31: #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 12:15:31: #1 tags after filtering in treatment: 9849096 INFO @ Tue, 02 Aug 2022 12:15:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:15:31: #1 finished! INFO @ Tue, 02 Aug 2022 12:15:31: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:15:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:15:32: #2 number of paired peaks: 1720 INFO @ Tue, 02 Aug 2022 12:15:32: start model_add_line... INFO @ Tue, 02 Aug 2022 12:15:32: start X-correlation... INFO @ Tue, 02 Aug 2022 12:15:32: end of X-cor INFO @ Tue, 02 Aug 2022 12:15:32: #2 finished! INFO @ Tue, 02 Aug 2022 12:15:32: #2 predicted fragment length is 296 bps INFO @ Tue, 02 Aug 2022 12:15:32: #2 alternative fragment length(s) may be 296 bps INFO @ Tue, 02 Aug 2022 12:15:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11638461/SRX11638461.10_model.r INFO @ Tue, 02 Aug 2022 12:15:32: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:15:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:15:36: 5000000 INFO @ Tue, 02 Aug 2022 12:15:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11638461/SRX11638461.05_peaks.xls INFO @ Tue, 02 Aug 2022 12:15:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11638461/SRX11638461.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:15:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11638461/SRX11638461.05_summits.bed INFO @ Tue, 02 Aug 2022 12:15:36: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (4754 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:15:41: 6000000 INFO @ Tue, 02 Aug 2022 12:15:46: 7000000 INFO @ Tue, 02 Aug 2022 12:15:51: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 12:15:55: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:15:56: 9000000 INFO @ Tue, 02 Aug 2022 12:16:00: #1 tag size is determined as 49 bps INFO @ Tue, 02 Aug 2022 12:16:00: #1 tag size = 49 INFO @ Tue, 02 Aug 2022 12:16:00: #1 total tags in treatment: 9849096 INFO @ Tue, 02 Aug 2022 12:16:00: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:16:00: #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 12:16:00: #1 tags after filtering in treatment: 9849096 INFO @ Tue, 02 Aug 2022 12:16:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:16:00: #1 finished! INFO @ Tue, 02 Aug 2022 12:16:00: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:16:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:16:01: #2 number of paired peaks: 1720 INFO @ Tue, 02 Aug 2022 12:16:01: start model_add_line... INFO @ Tue, 02 Aug 2022 12:16:01: start X-correlation... INFO @ Tue, 02 Aug 2022 12:16:01: end of X-cor INFO @ Tue, 02 Aug 2022 12:16:01: #2 finished! INFO @ Tue, 02 Aug 2022 12:16:01: #2 predicted fragment length is 296 bps INFO @ Tue, 02 Aug 2022 12:16:01: #2 alternative fragment length(s) may be 296 bps INFO @ Tue, 02 Aug 2022 12:16:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11638461/SRX11638461.20_model.r INFO @ Tue, 02 Aug 2022 12:16:01: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:16:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:16:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11638461/SRX11638461.10_peaks.xls INFO @ Tue, 02 Aug 2022 12:16:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11638461/SRX11638461.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:16:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11638461/SRX11638461.10_summits.bed INFO @ Tue, 02 Aug 2022 12:16:07: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (2831 records, 4 fields): 38 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 12:16:23: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:16:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11638461/SRX11638461.20_peaks.xls INFO @ Tue, 02 Aug 2022 12:16:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11638461/SRX11638461.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:16:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11638461/SRX11638461.20_summits.bed INFO @ Tue, 02 Aug 2022 12:16:34: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1310 records, 4 fields): 21 millis CompletedMACS2peakCalling