Job ID = 14168670 SRX = ERX3978877 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 19603960 spots for ERR3975946/ERR3975946.sra Written 19603960 spots for ERR3975946/ERR3975946.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169858 ("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: 01:19:20 19603960 reads; of these: 19603960 (100.00%) were paired; of these: 2308552 (11.78%) aligned concordantly 0 times 13130658 (66.98%) aligned concordantly exactly 1 time 4164750 (21.24%) aligned concordantly >1 times ---- 2308552 pairs aligned concordantly 0 times; of these: 447941 (19.40%) aligned discordantly 1 time ---- 1860611 pairs aligned 0 times concordantly or discordantly; of these: 3721222 mates make up the pairs; of these: 1813078 (48.72%) aligned 0 times 916002 (24.62%) aligned exactly 1 time 992142 (26.66%) aligned >1 times 95.38% overall alignment rate Time searching: 01:19:21 Overall time: 01:19:21 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 16 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] 10902384 / 17687719 = 0.6164 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 20:49:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978877/ERX3978877.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978877/ERX3978877.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978877/ERX3978877.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978877/ERX3978877.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 20:49:49: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:49:49: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:49:58: 1000000 INFO @ Fri, 10 Dec 2021 20:50:08: 2000000 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 20:50:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978877/ERX3978877.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978877/ERX3978877.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978877/ERX3978877.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978877/ERX3978877.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 20:50:18: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:50:18: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:50:18: 3000000 INFO @ Fri, 10 Dec 2021 20:50:28: 1000000 INFO @ Fri, 10 Dec 2021 20:50:28: 4000000 INFO @ Fri, 10 Dec 2021 20:50:38: 5000000 INFO @ Fri, 10 Dec 2021 20:50:38: 2000000 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 20:50:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978877/ERX3978877.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978877/ERX3978877.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978877/ERX3978877.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978877/ERX3978877.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 20:50:48: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:50:48: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:50:48: 6000000 INFO @ Fri, 10 Dec 2021 20:50:48: 3000000 INFO @ Fri, 10 Dec 2021 20:50:57: 7000000 INFO @ Fri, 10 Dec 2021 20:50:58: 1000000 INFO @ Fri, 10 Dec 2021 20:50:59: 4000000 INFO @ Fri, 10 Dec 2021 20:51:08: 8000000 INFO @ Fri, 10 Dec 2021 20:51:09: 2000000 INFO @ Fri, 10 Dec 2021 20:51:09: 5000000 INFO @ Fri, 10 Dec 2021 20:51:17: 9000000 INFO @ Fri, 10 Dec 2021 20:51:20: 6000000 INFO @ Fri, 10 Dec 2021 20:51:20: 3000000 INFO @ Fri, 10 Dec 2021 20:51:27: 10000000 INFO @ Fri, 10 Dec 2021 20:51:30: 7000000 INFO @ Fri, 10 Dec 2021 20:51:32: 4000000 INFO @ Fri, 10 Dec 2021 20:51:38: 11000000 INFO @ Fri, 10 Dec 2021 20:51:40: 8000000 INFO @ Fri, 10 Dec 2021 20:51:43: 5000000 INFO @ Fri, 10 Dec 2021 20:51:48: 12000000 INFO @ Fri, 10 Dec 2021 20:51:51: 9000000 INFO @ Fri, 10 Dec 2021 20:51:53: 6000000 INFO @ Fri, 10 Dec 2021 20:51:58: 13000000 INFO @ Fri, 10 Dec 2021 20:52:01: 10000000 INFO @ Fri, 10 Dec 2021 20:52:04: 7000000 INFO @ Fri, 10 Dec 2021 20:52:08: 14000000 INFO @ Fri, 10 Dec 2021 20:52:11: 11000000 INFO @ Fri, 10 Dec 2021 20:52:14: 8000000 INFO @ Fri, 10 Dec 2021 20:52:18: 15000000 INFO @ Fri, 10 Dec 2021 20:52:22: 12000000 INFO @ Fri, 10 Dec 2021 20:52:24: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 20:52:24: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 20:52:24: #1 total tags in treatment: 6599603 INFO @ Fri, 10 Dec 2021 20:52:24: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:52:24: #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 20:52:24: #1 tags after filtering in treatment: 6111062 INFO @ Fri, 10 Dec 2021 20:52:24: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 20:52:24: #1 finished! INFO @ Fri, 10 Dec 2021 20:52:24: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:52:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:52:25: #2 number of paired peaks: 1344 INFO @ Fri, 10 Dec 2021 20:52:25: start model_add_line... INFO @ Fri, 10 Dec 2021 20:52:25: start X-correlation... INFO @ Fri, 10 Dec 2021 20:52:25: end of X-cor INFO @ Fri, 10 Dec 2021 20:52:25: #2 finished! INFO @ Fri, 10 Dec 2021 20:52:25: #2 predicted fragment length is 182 bps INFO @ Fri, 10 Dec 2021 20:52:25: #2 alternative fragment length(s) may be 182 bps INFO @ Fri, 10 Dec 2021 20:52:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978877/ERX3978877.05_model.r INFO @ Fri, 10 Dec 2021 20:52:25: 9000000 INFO @ Fri, 10 Dec 2021 20:52:25: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:52:25: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 20:52:32: 13000000 INFO @ Fri, 10 Dec 2021 20:52:35: 10000000 INFO @ Fri, 10 Dec 2021 20:52:42: 14000000 INFO @ Fri, 10 Dec 2021 20:52:44: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:52:46: 11000000 INFO @ Fri, 10 Dec 2021 20:52:53: 15000000 INFO @ Fri, 10 Dec 2021 20:52:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978877/ERX3978877.05_peaks.xls INFO @ Fri, 10 Dec 2021 20:52:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978877/ERX3978877.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:52:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978877/ERX3978877.05_summits.bed INFO @ Fri, 10 Dec 2021 20:52:54: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (6979 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 20:52:56: 12000000 INFO @ Fri, 10 Dec 2021 20:52:59: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 20:52:59: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 20:52:59: #1 total tags in treatment: 6599603 INFO @ Fri, 10 Dec 2021 20:52:59: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:52:59: #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 20:52:59: #1 tags after filtering in treatment: 6111062 INFO @ Fri, 10 Dec 2021 20:52:59: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 20:52:59: #1 finished! INFO @ Fri, 10 Dec 2021 20:52:59: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:52:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:53:00: #2 number of paired peaks: 1344 INFO @ Fri, 10 Dec 2021 20:53:00: start model_add_line... INFO @ Fri, 10 Dec 2021 20:53:00: start X-correlation... INFO @ Fri, 10 Dec 2021 20:53:00: end of X-cor INFO @ Fri, 10 Dec 2021 20:53:00: #2 finished! INFO @ Fri, 10 Dec 2021 20:53:00: #2 predicted fragment length is 182 bps INFO @ Fri, 10 Dec 2021 20:53:00: #2 alternative fragment length(s) may be 182 bps INFO @ Fri, 10 Dec 2021 20:53:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978877/ERX3978877.10_model.r INFO @ Fri, 10 Dec 2021 20:53:00: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:53:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:53:06: 13000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 20:53:17: 14000000 INFO @ Fri, 10 Dec 2021 20:53:18: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:53:27: 15000000 INFO @ Fri, 10 Dec 2021 20:53:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978877/ERX3978877.10_peaks.xls INFO @ Fri, 10 Dec 2021 20:53:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978877/ERX3978877.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:53:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978877/ERX3978877.10_summits.bed INFO @ Fri, 10 Dec 2021 20:53:28: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3330 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 20:53:33: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 20:53:33: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 20:53:33: #1 total tags in treatment: 6599603 INFO @ Fri, 10 Dec 2021 20:53:33: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:53:33: #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 20:53:33: #1 tags after filtering in treatment: 6111062 INFO @ Fri, 10 Dec 2021 20:53:33: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 20:53:33: #1 finished! INFO @ Fri, 10 Dec 2021 20:53:33: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:53:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:53:33: #2 number of paired peaks: 1344 INFO @ Fri, 10 Dec 2021 20:53:33: start model_add_line... INFO @ Fri, 10 Dec 2021 20:53:34: start X-correlation... INFO @ Fri, 10 Dec 2021 20:53:34: end of X-cor INFO @ Fri, 10 Dec 2021 20:53:34: #2 finished! INFO @ Fri, 10 Dec 2021 20:53:34: #2 predicted fragment length is 182 bps INFO @ Fri, 10 Dec 2021 20:53:34: #2 alternative fragment length(s) may be 182 bps INFO @ Fri, 10 Dec 2021 20:53:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978877/ERX3978877.20_model.r INFO @ Fri, 10 Dec 2021 20:53:34: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:53:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:53:52: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:54:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978877/ERX3978877.20_peaks.xls INFO @ Fri, 10 Dec 2021 20:54:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978877/ERX3978877.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:54:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978877/ERX3978877.20_summits.bed INFO @ Fri, 10 Dec 2021 20:54:03: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1201 records, 4 fields): 8 millis CompletedMACS2peakCalling