Job ID = 14168831 SRX = ERX3978893 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21933820 spots for ERR3975962/ERR3975962.sra Written 21933820 spots for ERR3975962/ERR3975962.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170048 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 02:01:20 21933820 reads; of these: 21933820 (100.00%) were paired; of these: 2414763 (11.01%) aligned concordantly 0 times 15325515 (69.87%) aligned concordantly exactly 1 time 4193542 (19.12%) aligned concordantly >1 times ---- 2414763 pairs aligned concordantly 0 times; of these: 469081 (19.43%) aligned discordantly 1 time ---- 1945682 pairs aligned 0 times concordantly or discordantly; of these: 3891364 mates make up the pairs; of these: 1954732 (50.23%) aligned 0 times 800777 (20.58%) aligned exactly 1 time 1135855 (29.19%) aligned >1 times 95.54% overall alignment rate Time searching: 02:01:21 Overall time: 02:01:21 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 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] 15571923 / 19927695 = 0.7814 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 23:07:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978893/ERX3978893.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978893/ERX3978893.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978893/ERX3978893.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978893/ERX3978893.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 23:07:03: #1 read tag files... INFO @ Fri, 10 Dec 2021 23:07:03: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 23:07:08: 1000000 INFO @ Fri, 10 Dec 2021 23:07:14: 2000000 INFO @ Fri, 10 Dec 2021 23:07:19: 3000000 INFO @ Fri, 10 Dec 2021 23:07:25: 4000000 INFO @ Fri, 10 Dec 2021 23:07:30: 5000000 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 23:07:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978893/ERX3978893.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978893/ERX3978893.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978893/ERX3978893.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978893/ERX3978893.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 23:07:33: #1 read tag files... INFO @ Fri, 10 Dec 2021 23:07:33: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 23:07:36: 6000000 INFO @ Fri, 10 Dec 2021 23:07:40: 1000000 INFO @ Fri, 10 Dec 2021 23:07:43: 7000000 INFO @ Fri, 10 Dec 2021 23:07:48: 2000000 INFO @ Fri, 10 Dec 2021 23:07:50: 8000000 INFO @ Fri, 10 Dec 2021 23:07:56: 3000000 INFO @ Fri, 10 Dec 2021 23:07:57: 9000000 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 23:08:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978893/ERX3978893.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978893/ERX3978893.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978893/ERX3978893.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978893/ERX3978893.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 23:08:03: #1 read tag files... INFO @ Fri, 10 Dec 2021 23:08:03: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 23:08:04: 4000000 INFO @ Fri, 10 Dec 2021 23:08:04: 10000000 INFO @ Fri, 10 Dec 2021 23:08:09: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 23:08:09: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 23:08:09: #1 total tags in treatment: 4238196 INFO @ Fri, 10 Dec 2021 23:08:09: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 23:08:09: #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 23:08:09: #1 tags after filtering in treatment: 3799964 INFO @ Fri, 10 Dec 2021 23:08:09: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 10 Dec 2021 23:08:09: #1 finished! INFO @ Fri, 10 Dec 2021 23:08:09: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 23:08:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 23:08:10: 1000000 INFO @ Fri, 10 Dec 2021 23:08:10: #2 number of paired peaks: 4617 INFO @ Fri, 10 Dec 2021 23:08:10: start model_add_line... INFO @ Fri, 10 Dec 2021 23:08:10: start X-correlation... INFO @ Fri, 10 Dec 2021 23:08:10: end of X-cor INFO @ Fri, 10 Dec 2021 23:08:10: #2 finished! INFO @ Fri, 10 Dec 2021 23:08:10: #2 predicted fragment length is 199 bps INFO @ Fri, 10 Dec 2021 23:08:10: #2 alternative fragment length(s) may be 199 bps INFO @ Fri, 10 Dec 2021 23:08:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978893/ERX3978893.05_model.r INFO @ Fri, 10 Dec 2021 23:08:10: #3 Call peaks... INFO @ Fri, 10 Dec 2021 23:08:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 23:08:11: 5000000 INFO @ Fri, 10 Dec 2021 23:08:16: 2000000 INFO @ Fri, 10 Dec 2021 23:08:19: 6000000 INFO @ Fri, 10 Dec 2021 23:08:20: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 23:08:23: 3000000 INFO @ Fri, 10 Dec 2021 23:08:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978893/ERX3978893.05_peaks.xls INFO @ Fri, 10 Dec 2021 23:08:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978893/ERX3978893.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 23:08:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978893/ERX3978893.05_summits.bed INFO @ Fri, 10 Dec 2021 23:08:25: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9345 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 23:08:27: 7000000 INFO @ Fri, 10 Dec 2021 23:08:30: 4000000 INFO @ Fri, 10 Dec 2021 23:08:35: 8000000 INFO @ Fri, 10 Dec 2021 23:08:36: 5000000 INFO @ Fri, 10 Dec 2021 23:08:43: 6000000 INFO @ Fri, 10 Dec 2021 23:08:43: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 23:08:50: 7000000 INFO @ Fri, 10 Dec 2021 23:08:52: 10000000 INFO @ Fri, 10 Dec 2021 23:08:57: 8000000 INFO @ Fri, 10 Dec 2021 23:08:57: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 23:08:57: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 23:08:57: #1 total tags in treatment: 4238196 INFO @ Fri, 10 Dec 2021 23:08:57: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 23:08:57: #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 23:08:58: #1 tags after filtering in treatment: 3799964 INFO @ Fri, 10 Dec 2021 23:08:58: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 10 Dec 2021 23:08:58: #1 finished! INFO @ Fri, 10 Dec 2021 23:08:58: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 23:08:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 23:08:58: #2 number of paired peaks: 4617 INFO @ Fri, 10 Dec 2021 23:08:58: start model_add_line... INFO @ Fri, 10 Dec 2021 23:08:58: start X-correlation... INFO @ Fri, 10 Dec 2021 23:08:58: end of X-cor INFO @ Fri, 10 Dec 2021 23:08:58: #2 finished! INFO @ Fri, 10 Dec 2021 23:08:58: #2 predicted fragment length is 199 bps INFO @ Fri, 10 Dec 2021 23:08:58: #2 alternative fragment length(s) may be 199 bps INFO @ Fri, 10 Dec 2021 23:08:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978893/ERX3978893.10_model.r INFO @ Fri, 10 Dec 2021 23:08:58: #3 Call peaks... INFO @ Fri, 10 Dec 2021 23:08:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 23:09:03: 9000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 23:09:07: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 23:09:09: 10000000 INFO @ Fri, 10 Dec 2021 23:09:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978893/ERX3978893.10_peaks.xls INFO @ Fri, 10 Dec 2021 23:09:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978893/ERX3978893.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 23:09:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978893/ERX3978893.10_summits.bed INFO @ Fri, 10 Dec 2021 23:09:12: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5920 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 23:09:14: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 23:09:14: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 23:09:14: #1 total tags in treatment: 4238196 INFO @ Fri, 10 Dec 2021 23:09:14: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 23:09:14: #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 23:09:14: #1 tags after filtering in treatment: 3799964 INFO @ Fri, 10 Dec 2021 23:09:14: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 10 Dec 2021 23:09:14: #1 finished! INFO @ Fri, 10 Dec 2021 23:09:14: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 23:09:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 23:09:15: #2 number of paired peaks: 4617 INFO @ Fri, 10 Dec 2021 23:09:15: start model_add_line... INFO @ Fri, 10 Dec 2021 23:09:15: start X-correlation... INFO @ Fri, 10 Dec 2021 23:09:15: end of X-cor INFO @ Fri, 10 Dec 2021 23:09:15: #2 finished! INFO @ Fri, 10 Dec 2021 23:09:15: #2 predicted fragment length is 199 bps INFO @ Fri, 10 Dec 2021 23:09:15: #2 alternative fragment length(s) may be 199 bps INFO @ Fri, 10 Dec 2021 23:09:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978893/ERX3978893.20_model.r INFO @ Fri, 10 Dec 2021 23:09:15: #3 Call peaks... INFO @ Fri, 10 Dec 2021 23:09:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 23:09:24: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 23:09:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978893/ERX3978893.20_peaks.xls INFO @ Fri, 10 Dec 2021 23:09:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978893/ERX3978893.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 23:09:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978893/ERX3978893.20_summits.bed INFO @ Fri, 10 Dec 2021 23:09:28: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (2725 records, 4 fields): 5 millis CompletedMACS2peakCalling