Job ID = 6626552 SRX = SRX6813089 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 10935424 spots for SRR10080053/SRR10080053.sra Written 10935424 spots for SRR10080053/SRR10080053.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626679 ("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: 00:02:24 10935424 reads; of these: 10935424 (100.00%) were unpaired; of these: 2691022 (24.61%) aligned 0 times 7079582 (64.74%) aligned exactly 1 time 1164820 (10.65%) aligned >1 times 75.39% overall alignment rate Time searching: 00:02:24 Overall time: 00:02:24 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_rmdupse_core] 1124213 / 8244402 = 0.1364 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:35:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813089/SRX6813089.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813089/SRX6813089.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813089/SRX6813089.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813089/SRX6813089.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, 14 Jul 2020 07:35:28: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:35:28: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:35:33: 1000000 INFO @ Tue, 14 Jul 2020 07:35:38: 2000000 INFO @ Tue, 14 Jul 2020 07:35:42: 3000000 INFO @ Tue, 14 Jul 2020 07:35:47: 4000000 INFO @ Tue, 14 Jul 2020 07:35:52: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:35:56: 6000000 INFO @ Tue, 14 Jul 2020 07:35:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813089/SRX6813089.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813089/SRX6813089.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813089/SRX6813089.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813089/SRX6813089.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, 14 Jul 2020 07:35:58: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:35:58: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:36:01: 7000000 INFO @ Tue, 14 Jul 2020 07:36:02: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:36:02: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:36:02: #1 total tags in treatment: 7120189 INFO @ Tue, 14 Jul 2020 07:36:02: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:36:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:36:02: #1 tags after filtering in treatment: 7120189 INFO @ Tue, 14 Jul 2020 07:36:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:36:02: #1 finished! INFO @ Tue, 14 Jul 2020 07:36:02: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:36:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:36:03: #2 number of paired peaks: 7754 INFO @ Tue, 14 Jul 2020 07:36:03: start model_add_line... INFO @ Tue, 14 Jul 2020 07:36:03: start X-correlation... INFO @ Tue, 14 Jul 2020 07:36:03: end of X-cor INFO @ Tue, 14 Jul 2020 07:36:03: #2 finished! INFO @ Tue, 14 Jul 2020 07:36:03: #2 predicted fragment length is 238 bps INFO @ Tue, 14 Jul 2020 07:36:03: #2 alternative fragment length(s) may be 238 bps INFO @ Tue, 14 Jul 2020 07:36:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813089/SRX6813089.05_model.r INFO @ Tue, 14 Jul 2020 07:36:03: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:36:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:36:04: 1000000 INFO @ Tue, 14 Jul 2020 07:36:09: 2000000 INFO @ Tue, 14 Jul 2020 07:36:14: 3000000 INFO @ Tue, 14 Jul 2020 07:36:19: 4000000 INFO @ Tue, 14 Jul 2020 07:36:25: 5000000 INFO @ Tue, 14 Jul 2020 07:36:25: #3 Call peaks for each chromosome... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:36:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813089/SRX6813089.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813089/SRX6813089.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813089/SRX6813089.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813089/SRX6813089.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, 14 Jul 2020 07:36:28: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:36:28: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:36:30: 6000000 INFO @ Tue, 14 Jul 2020 07:36:34: 1000000 INFO @ Tue, 14 Jul 2020 07:36:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813089/SRX6813089.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:36:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813089/SRX6813089.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:36:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813089/SRX6813089.05_summits.bed INFO @ Tue, 14 Jul 2020 07:36:34: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3876 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:36:36: 7000000 INFO @ Tue, 14 Jul 2020 07:36:37: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:36:37: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:36:37: #1 total tags in treatment: 7120189 INFO @ Tue, 14 Jul 2020 07:36:37: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:36:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:36:37: #1 tags after filtering in treatment: 7120189 INFO @ Tue, 14 Jul 2020 07:36:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:36:37: #1 finished! INFO @ Tue, 14 Jul 2020 07:36:37: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:36:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:36:38: #2 number of paired peaks: 7754 INFO @ Tue, 14 Jul 2020 07:36:38: start model_add_line... INFO @ Tue, 14 Jul 2020 07:36:38: start X-correlation... INFO @ Tue, 14 Jul 2020 07:36:38: end of X-cor INFO @ Tue, 14 Jul 2020 07:36:38: #2 finished! INFO @ Tue, 14 Jul 2020 07:36:38: #2 predicted fragment length is 238 bps INFO @ Tue, 14 Jul 2020 07:36:38: #2 alternative fragment length(s) may be 238 bps INFO @ Tue, 14 Jul 2020 07:36:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813089/SRX6813089.10_model.r INFO @ Tue, 14 Jul 2020 07:36:38: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:36:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:36:39: 2000000 INFO @ Tue, 14 Jul 2020 07:36:45: 3000000 INFO @ Tue, 14 Jul 2020 07:36:50: 4000000 INFO @ Tue, 14 Jul 2020 07:36:56: 5000000 INFO @ Tue, 14 Jul 2020 07:37:01: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:37:02: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:37:06: 7000000 INFO @ Tue, 14 Jul 2020 07:37:07: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:37:07: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:37:07: #1 total tags in treatment: 7120189 INFO @ Tue, 14 Jul 2020 07:37:07: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:37:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:37:07: #1 tags after filtering in treatment: 7120189 INFO @ Tue, 14 Jul 2020 07:37:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:37:07: #1 finished! INFO @ Tue, 14 Jul 2020 07:37:07: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:37:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:37:08: #2 number of paired peaks: 7754 INFO @ Tue, 14 Jul 2020 07:37:08: start model_add_line... INFO @ Tue, 14 Jul 2020 07:37:08: start X-correlation... INFO @ Tue, 14 Jul 2020 07:37:08: end of X-cor INFO @ Tue, 14 Jul 2020 07:37:08: #2 finished! INFO @ Tue, 14 Jul 2020 07:37:08: #2 predicted fragment length is 238 bps INFO @ Tue, 14 Jul 2020 07:37:08: #2 alternative fragment length(s) may be 238 bps INFO @ Tue, 14 Jul 2020 07:37:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813089/SRX6813089.20_model.r INFO @ Tue, 14 Jul 2020 07:37:08: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:37:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:37:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813089/SRX6813089.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:37:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813089/SRX6813089.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:37:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813089/SRX6813089.10_summits.bed INFO @ Tue, 14 Jul 2020 07:37:11: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1851 records, 4 fields): 10 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:37:32: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:37:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813089/SRX6813089.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:37:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813089/SRX6813089.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:37:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813089/SRX6813089.20_summits.bed INFO @ Tue, 14 Jul 2020 07:37:41: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (762 records, 4 fields): 8 millis CompletedMACS2peakCalling