Job ID = 14166963 SRX = SRX7723701 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 23891099 spots for SRR11084657/SRR11084657.sra Written 23891099 spots for SRR11084657/SRR11084657.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167282 ("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: 00:05:58 23891099 reads; of these: 23891099 (100.00%) were unpaired; of these: 10649527 (44.58%) aligned 0 times 12317973 (51.56%) aligned exactly 1 time 923599 (3.87%) aligned >1 times 55.42% overall alignment rate Time searching: 00:05:58 Overall time: 00:05:58 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] 7445487 / 13241572 = 0.5623 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 08:19:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723701/SRX7723701.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723701/SRX7723701.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723701/SRX7723701.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723701/SRX7723701.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 08:19:16: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:19:16: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:19:22: 1000000 INFO @ Fri, 10 Dec 2021 08:19:28: 2000000 INFO @ Fri, 10 Dec 2021 08:19:34: 3000000 INFO @ Fri, 10 Dec 2021 08:19:40: 4000000 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 08:19:45: 5000000 INFO @ Fri, 10 Dec 2021 08:19:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723701/SRX7723701.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723701/SRX7723701.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723701/SRX7723701.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723701/SRX7723701.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 08:19:46: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:19:46: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:19:50: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 08:19:50: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 08:19:50: #1 total tags in treatment: 5796085 INFO @ Fri, 10 Dec 2021 08:19:50: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:19:50: #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 08:19:51: #1 tags after filtering in treatment: 5796085 INFO @ Fri, 10 Dec 2021 08:19:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 08:19:51: #1 finished! INFO @ Fri, 10 Dec 2021 08:19:51: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:19:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:19:51: #2 number of paired peaks: 9270 INFO @ Fri, 10 Dec 2021 08:19:51: start model_add_line... INFO @ Fri, 10 Dec 2021 08:19:51: start X-correlation... INFO @ Fri, 10 Dec 2021 08:19:51: end of X-cor INFO @ Fri, 10 Dec 2021 08:19:51: #2 finished! INFO @ Fri, 10 Dec 2021 08:19:51: #2 predicted fragment length is 155 bps INFO @ Fri, 10 Dec 2021 08:19:51: #2 alternative fragment length(s) may be 155 bps INFO @ Fri, 10 Dec 2021 08:19:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723701/SRX7723701.05_model.r INFO @ Fri, 10 Dec 2021 08:19:51: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:19:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:19:53: 1000000 INFO @ Fri, 10 Dec 2021 08:19:59: 2000000 INFO @ Fri, 10 Dec 2021 08:20:04: 3000000 INFO @ Fri, 10 Dec 2021 08:20:06: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:20:10: 4000000 INFO @ Fri, 10 Dec 2021 08:20:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723701/SRX7723701.05_peaks.xls INFO @ Fri, 10 Dec 2021 08:20:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723701/SRX7723701.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:20:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723701/SRX7723701.05_summits.bed INFO @ Fri, 10 Dec 2021 08:20:13: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8222 records, 4 fields): 9 millis CompletedMACS2peakCalling 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 08:20:16: 5000000 INFO @ Fri, 10 Dec 2021 08:20:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723701/SRX7723701.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723701/SRX7723701.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723701/SRX7723701.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723701/SRX7723701.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 08:20:16: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:20:16: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:20:21: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 08:20:21: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 08:20:21: #1 total tags in treatment: 5796085 INFO @ Fri, 10 Dec 2021 08:20:21: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:20:21: #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 08:20:21: #1 tags after filtering in treatment: 5796085 INFO @ Fri, 10 Dec 2021 08:20:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 08:20:21: #1 finished! INFO @ Fri, 10 Dec 2021 08:20:21: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:20:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:20:22: #2 number of paired peaks: 9270 INFO @ Fri, 10 Dec 2021 08:20:22: start model_add_line... INFO @ Fri, 10 Dec 2021 08:20:22: start X-correlation... INFO @ Fri, 10 Dec 2021 08:20:22: end of X-cor INFO @ Fri, 10 Dec 2021 08:20:22: #2 finished! INFO @ Fri, 10 Dec 2021 08:20:22: #2 predicted fragment length is 155 bps INFO @ Fri, 10 Dec 2021 08:20:22: #2 alternative fragment length(s) may be 155 bps INFO @ Fri, 10 Dec 2021 08:20:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723701/SRX7723701.10_model.r INFO @ Fri, 10 Dec 2021 08:20:22: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:20:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:20:23: 1000000 INFO @ Fri, 10 Dec 2021 08:20:29: 2000000 INFO @ Fri, 10 Dec 2021 08:20:35: 3000000 INFO @ Fri, 10 Dec 2021 08:20:37: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:20:41: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 08:20:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723701/SRX7723701.10_peaks.xls INFO @ Fri, 10 Dec 2021 08:20:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723701/SRX7723701.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:20:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723701/SRX7723701.10_summits.bed INFO @ Fri, 10 Dec 2021 08:20:44: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7123 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 08:20:47: 5000000 INFO @ Fri, 10 Dec 2021 08:20:51: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 08:20:51: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 08:20:51: #1 total tags in treatment: 5796085 INFO @ Fri, 10 Dec 2021 08:20:51: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:20:51: #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 08:20:52: #1 tags after filtering in treatment: 5796085 INFO @ Fri, 10 Dec 2021 08:20:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 08:20:52: #1 finished! INFO @ Fri, 10 Dec 2021 08:20:52: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:20:52: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 08:20:52: #2 number of paired peaks: 9270 INFO @ Fri, 10 Dec 2021 08:20:52: start model_add_line... INFO @ Fri, 10 Dec 2021 08:20:53: start X-correlation... INFO @ Fri, 10 Dec 2021 08:20:53: end of X-cor INFO @ Fri, 10 Dec 2021 08:20:53: #2 finished! INFO @ Fri, 10 Dec 2021 08:20:53: #2 predicted fragment length is 155 bps INFO @ Fri, 10 Dec 2021 08:20:53: #2 alternative fragment length(s) may be 155 bps INFO @ Fri, 10 Dec 2021 08:20:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723701/SRX7723701.20_model.r INFO @ Fri, 10 Dec 2021 08:20:53: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:20:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:21:07: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:21:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723701/SRX7723701.20_peaks.xls INFO @ Fri, 10 Dec 2021 08:21:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723701/SRX7723701.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:21:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723701/SRX7723701.20_summits.bed INFO @ Fri, 10 Dec 2021 08:21:14: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (5534 records, 4 fields): 6 millis CompletedMACS2peakCalling