Job ID = 14171938 SRX = SRX9427704 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 12248813 spots for SRR12975511/SRR12975511.sra Written 12248813 spots for SRR12975511/SRR12975511.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172409 ("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: 00:05:53 12248813 reads; of these: 12248813 (100.00%) were unpaired; of these: 225577 (1.84%) aligned 0 times 2970878 (24.25%) aligned exactly 1 time 9052358 (73.90%) aligned >1 times 98.16% overall alignment rate Time searching: 00:05:53 Overall time: 00:05:53 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] 2689879 / 12023236 = 0.2237 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 @ Sat, 11 Dec 2021 13:36:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9427704/SRX9427704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9427704/SRX9427704.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9427704/SRX9427704.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9427704/SRX9427704.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 @ Sat, 11 Dec 2021 13:36:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:36:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:36:51: 1000000 INFO @ Sat, 11 Dec 2021 13:36:57: 2000000 INFO @ Sat, 11 Dec 2021 13:37:03: 3000000 INFO @ Sat, 11 Dec 2021 13:37:09: 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 @ Sat, 11 Dec 2021 13:37:14: 5000000 INFO @ Sat, 11 Dec 2021 13:37:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9427704/SRX9427704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9427704/SRX9427704.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9427704/SRX9427704.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9427704/SRX9427704.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 @ Sat, 11 Dec 2021 13:37:15: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:37:15: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:37:20: 6000000 INFO @ Sat, 11 Dec 2021 13:37:22: 1000000 INFO @ Sat, 11 Dec 2021 13:37:27: 7000000 INFO @ Sat, 11 Dec 2021 13:37:29: 2000000 INFO @ Sat, 11 Dec 2021 13:37:34: 8000000 INFO @ Sat, 11 Dec 2021 13:37:36: 3000000 INFO @ Sat, 11 Dec 2021 13:37:40: 9000000 INFO @ Sat, 11 Dec 2021 13:37:43: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:37:43: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:37:43: #1 total tags in treatment: 9333357 INFO @ Sat, 11 Dec 2021 13:37:43: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:37:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:37:43: #1 tags after filtering in treatment: 9333357 INFO @ Sat, 11 Dec 2021 13:37:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:37:43: #1 finished! INFO @ Sat, 11 Dec 2021 13:37:43: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:37:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:37:43: 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 @ Sat, 11 Dec 2021 13:37:44: #2 number of paired peaks: 5903 INFO @ Sat, 11 Dec 2021 13:37:44: start model_add_line... INFO @ Sat, 11 Dec 2021 13:37:44: start X-correlation... INFO @ Sat, 11 Dec 2021 13:37:44: end of X-cor INFO @ Sat, 11 Dec 2021 13:37:44: #2 finished! INFO @ Sat, 11 Dec 2021 13:37:44: #2 predicted fragment length is 102 bps INFO @ Sat, 11 Dec 2021 13:37:44: #2 alternative fragment length(s) may be 4,102 bps INFO @ Sat, 11 Dec 2021 13:37:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9427704/SRX9427704.05_model.r INFO @ Sat, 11 Dec 2021 13:37:44: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:37:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:37:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9427704/SRX9427704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9427704/SRX9427704.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9427704/SRX9427704.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9427704/SRX9427704.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 @ Sat, 11 Dec 2021 13:37:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:37:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:37:49: 5000000 INFO @ Sat, 11 Dec 2021 13:37:52: 1000000 INFO @ Sat, 11 Dec 2021 13:37:56: 6000000 INFO @ Sat, 11 Dec 2021 13:38:00: 2000000 INFO @ Sat, 11 Dec 2021 13:38:03: 7000000 INFO @ Sat, 11 Dec 2021 13:38:05: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:38:06: 3000000 INFO @ Sat, 11 Dec 2021 13:38:10: 8000000 INFO @ Sat, 11 Dec 2021 13:38:13: 4000000 INFO @ Sat, 11 Dec 2021 13:38:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9427704/SRX9427704.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:38:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9427704/SRX9427704.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:38:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9427704/SRX9427704.05_summits.bed INFO @ Sat, 11 Dec 2021 13:38:15: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (12854 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:38:16: 9000000 INFO @ Sat, 11 Dec 2021 13:38:19: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:38:19: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:38:19: #1 total tags in treatment: 9333357 INFO @ Sat, 11 Dec 2021 13:38:19: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:38:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:38:19: #1 tags after filtering in treatment: 9333357 INFO @ Sat, 11 Dec 2021 13:38:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:38:19: #1 finished! INFO @ Sat, 11 Dec 2021 13:38:19: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:38:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:38:20: #2 number of paired peaks: 5903 INFO @ Sat, 11 Dec 2021 13:38:20: start model_add_line... INFO @ Sat, 11 Dec 2021 13:38:20: start X-correlation... INFO @ Sat, 11 Dec 2021 13:38:20: end of X-cor INFO @ Sat, 11 Dec 2021 13:38:20: #2 finished! INFO @ Sat, 11 Dec 2021 13:38:20: #2 predicted fragment length is 102 bps INFO @ Sat, 11 Dec 2021 13:38:20: #2 alternative fragment length(s) may be 4,102 bps INFO @ Sat, 11 Dec 2021 13:38:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9427704/SRX9427704.10_model.r INFO @ Sat, 11 Dec 2021 13:38:20: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:38:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:38:20: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:38:27: 6000000 INFO @ Sat, 11 Dec 2021 13:38:33: 7000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:38:40: 8000000 INFO @ Sat, 11 Dec 2021 13:38:40: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:38:46: 9000000 INFO @ Sat, 11 Dec 2021 13:38:48: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:38:48: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:38:48: #1 total tags in treatment: 9333357 INFO @ Sat, 11 Dec 2021 13:38:48: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:38:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:38:48: #1 tags after filtering in treatment: 9333357 INFO @ Sat, 11 Dec 2021 13:38:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:38:48: #1 finished! INFO @ Sat, 11 Dec 2021 13:38:48: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:38:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:38:49: #2 number of paired peaks: 5903 INFO @ Sat, 11 Dec 2021 13:38:49: start model_add_line... INFO @ Sat, 11 Dec 2021 13:38:49: start X-correlation... INFO @ Sat, 11 Dec 2021 13:38:49: end of X-cor INFO @ Sat, 11 Dec 2021 13:38:49: #2 finished! INFO @ Sat, 11 Dec 2021 13:38:49: #2 predicted fragment length is 102 bps INFO @ Sat, 11 Dec 2021 13:38:49: #2 alternative fragment length(s) may be 4,102 bps INFO @ Sat, 11 Dec 2021 13:38:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9427704/SRX9427704.20_model.r INFO @ Sat, 11 Dec 2021 13:38:49: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:38:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:38:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9427704/SRX9427704.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:38:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9427704/SRX9427704.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:38:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9427704/SRX9427704.10_summits.bed INFO @ Sat, 11 Dec 2021 13:38:50: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6415 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:39:10: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:39:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9427704/SRX9427704.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:39:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9427704/SRX9427704.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:39:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9427704/SRX9427704.20_summits.bed INFO @ Sat, 11 Dec 2021 13:39:21: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1784 records, 4 fields): 3 millis CompletedMACS2peakCalling