Job ID = 14168102 SRX = ERX3978827 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 25567056 spots for ERR3975896/ERR3975896.sra Written 25567056 spots for ERR3975896/ERR3975896.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169169 ("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: 01:35:41 25567056 reads; of these: 25567056 (100.00%) were paired; of these: 3028335 (11.84%) aligned concordantly 0 times 17327679 (67.77%) aligned concordantly exactly 1 time 5211042 (20.38%) aligned concordantly >1 times ---- 3028335 pairs aligned concordantly 0 times; of these: 473387 (15.63%) aligned discordantly 1 time ---- 2554948 pairs aligned 0 times concordantly or discordantly; of these: 5109896 mates make up the pairs; of these: 2619398 (51.26%) aligned 0 times 1104104 (21.61%) aligned exactly 1 time 1386394 (27.13%) aligned >1 times 94.88% overall alignment rate Time searching: 01:35:41 Overall time: 01:35:41 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 20 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] 18154744 / 22899443 = 0.7928 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 17:12:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978827/ERX3978827.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978827/ERX3978827.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978827/ERX3978827.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978827/ERX3978827.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 17:12:15: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:12:15: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:12:22: 1000000 INFO @ Fri, 10 Dec 2021 17:12:30: 2000000 INFO @ Fri, 10 Dec 2021 17:12:37: 3000000 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 17:12:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978827/ERX3978827.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978827/ERX3978827.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978827/ERX3978827.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978827/ERX3978827.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 17:12:44: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:12:44: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:12:44: 4000000 INFO @ Fri, 10 Dec 2021 17:12:52: 5000000 INFO @ Fri, 10 Dec 2021 17:12:52: 1000000 INFO @ Fri, 10 Dec 2021 17:12:59: 6000000 INFO @ Fri, 10 Dec 2021 17:13:00: 2000000 INFO @ Fri, 10 Dec 2021 17:13:07: 7000000 INFO @ Fri, 10 Dec 2021 17:13:08: 3000000 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 17:13:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978827/ERX3978827.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978827/ERX3978827.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978827/ERX3978827.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978827/ERX3978827.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 17:13:14: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:13:14: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:13:15: 8000000 INFO @ Fri, 10 Dec 2021 17:13:16: 4000000 INFO @ Fri, 10 Dec 2021 17:13:22: 1000000 INFO @ Fri, 10 Dec 2021 17:13:24: 9000000 INFO @ Fri, 10 Dec 2021 17:13:24: 5000000 INFO @ Fri, 10 Dec 2021 17:13:31: 2000000 INFO @ Fri, 10 Dec 2021 17:13:32: 6000000 INFO @ Fri, 10 Dec 2021 17:13:33: 10000000 INFO @ Fri, 10 Dec 2021 17:13:40: 3000000 INFO @ Fri, 10 Dec 2021 17:13:40: 7000000 INFO @ Fri, 10 Dec 2021 17:13:42: 11000000 INFO @ Fri, 10 Dec 2021 17:13:48: 4000000 INFO @ Fri, 10 Dec 2021 17:13:49: 8000000 INFO @ Fri, 10 Dec 2021 17:13:50: 12000000 INFO @ Fri, 10 Dec 2021 17:13:52: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 17:13:52: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 17:13:52: #1 total tags in treatment: 4746959 INFO @ Fri, 10 Dec 2021 17:13:52: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:13:52: #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 17:13:52: #1 tags after filtering in treatment: 4268534 INFO @ Fri, 10 Dec 2021 17:13:52: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 10 Dec 2021 17:13:52: #1 finished! INFO @ Fri, 10 Dec 2021 17:13:52: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:13:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:13:53: #2 number of paired peaks: 2698 INFO @ Fri, 10 Dec 2021 17:13:53: start model_add_line... INFO @ Fri, 10 Dec 2021 17:13:53: start X-correlation... INFO @ Fri, 10 Dec 2021 17:13:53: end of X-cor INFO @ Fri, 10 Dec 2021 17:13:53: #2 finished! INFO @ Fri, 10 Dec 2021 17:13:53: #2 predicted fragment length is 155 bps INFO @ Fri, 10 Dec 2021 17:13:53: #2 alternative fragment length(s) may be 155 bps INFO @ Fri, 10 Dec 2021 17:13:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978827/ERX3978827.05_model.r INFO @ Fri, 10 Dec 2021 17:13:53: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:13:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:13:56: 5000000 INFO @ Fri, 10 Dec 2021 17:13:57: 9000000 INFO @ Fri, 10 Dec 2021 17:14:03: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:14:04: 6000000 INFO @ Fri, 10 Dec 2021 17:14:05: 10000000 INFO @ Fri, 10 Dec 2021 17:14:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978827/ERX3978827.05_peaks.xls INFO @ Fri, 10 Dec 2021 17:14:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978827/ERX3978827.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:14:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978827/ERX3978827.05_summits.bed INFO @ Fri, 10 Dec 2021 17:14:09: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9301 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:14:12: 7000000 INFO @ Fri, 10 Dec 2021 17:14:13: 11000000 INFO @ Fri, 10 Dec 2021 17:14:20: 8000000 INFO @ Fri, 10 Dec 2021 17:14:21: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 17:14:23: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 17:14:23: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 17:14:23: #1 total tags in treatment: 4746959 INFO @ Fri, 10 Dec 2021 17:14:23: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:14:23: #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 17:14:23: #1 tags after filtering in treatment: 4268534 INFO @ Fri, 10 Dec 2021 17:14:23: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 10 Dec 2021 17:14:23: #1 finished! INFO @ Fri, 10 Dec 2021 17:14:23: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:14:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:14:23: #2 number of paired peaks: 2698 INFO @ Fri, 10 Dec 2021 17:14:23: start model_add_line... INFO @ Fri, 10 Dec 2021 17:14:23: start X-correlation... INFO @ Fri, 10 Dec 2021 17:14:23: end of X-cor INFO @ Fri, 10 Dec 2021 17:14:23: #2 finished! INFO @ Fri, 10 Dec 2021 17:14:23: #2 predicted fragment length is 155 bps INFO @ Fri, 10 Dec 2021 17:14:23: #2 alternative fragment length(s) may be 155 bps INFO @ Fri, 10 Dec 2021 17:14:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978827/ERX3978827.10_model.r INFO @ Fri, 10 Dec 2021 17:14:23: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:14:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:14:29: 9000000 INFO @ Fri, 10 Dec 2021 17:14:33: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:14:36: 10000000 INFO @ Fri, 10 Dec 2021 17:14:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978827/ERX3978827.10_peaks.xls INFO @ Fri, 10 Dec 2021 17:14:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978827/ERX3978827.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:14:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978827/ERX3978827.10_summits.bed INFO @ Fri, 10 Dec 2021 17:14:39: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5001 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:14:44: 11000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 17:14:52: 12000000 INFO @ Fri, 10 Dec 2021 17:14:53: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 17:14:53: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 17:14:53: #1 total tags in treatment: 4746959 INFO @ Fri, 10 Dec 2021 17:14:53: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:14:53: #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 17:14:54: #1 tags after filtering in treatment: 4268534 INFO @ Fri, 10 Dec 2021 17:14:54: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 10 Dec 2021 17:14:54: #1 finished! INFO @ Fri, 10 Dec 2021 17:14:54: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:14:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:14:54: #2 number of paired peaks: 2698 INFO @ Fri, 10 Dec 2021 17:14:54: start model_add_line... INFO @ Fri, 10 Dec 2021 17:14:54: start X-correlation... INFO @ Fri, 10 Dec 2021 17:14:54: end of X-cor INFO @ Fri, 10 Dec 2021 17:14:54: #2 finished! INFO @ Fri, 10 Dec 2021 17:14:54: #2 predicted fragment length is 155 bps INFO @ Fri, 10 Dec 2021 17:14:54: #2 alternative fragment length(s) may be 155 bps INFO @ Fri, 10 Dec 2021 17:14:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978827/ERX3978827.20_model.r INFO @ Fri, 10 Dec 2021 17:14:54: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:14:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:15:04: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:15:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978827/ERX3978827.20_peaks.xls INFO @ Fri, 10 Dec 2021 17:15:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978827/ERX3978827.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:15:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978827/ERX3978827.20_summits.bed INFO @ Fri, 10 Dec 2021 17:15:10: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1742 records, 4 fields): 5 millis CompletedMACS2peakCalling