Job ID = 14168717 SRX = ERX3978880 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 15067379 spots for ERR3975949/ERR3975949.sra Written 15067379 spots for ERR3975949/ERR3975949.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169852 ("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: 00:42:05 15067379 reads; of these: 15067379 (100.00%) were paired; of these: 2379289 (15.79%) aligned concordantly 0 times 10353927 (68.72%) aligned concordantly exactly 1 time 2334163 (15.49%) aligned concordantly >1 times ---- 2379289 pairs aligned concordantly 0 times; of these: 932644 (39.20%) aligned discordantly 1 time ---- 1446645 pairs aligned 0 times concordantly or discordantly; of these: 2893290 mates make up the pairs; of these: 1339284 (46.29%) aligned 0 times 737204 (25.48%) aligned exactly 1 time 816802 (28.23%) aligned >1 times 95.56% overall alignment rate Time searching: 00:42:05 Overall time: 00:42:05 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 12 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] 9308269 / 13584104 = 0.6852 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 20:34:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978880/ERX3978880.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978880/ERX3978880.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978880/ERX3978880.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978880/ERX3978880.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 20:34:57: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:34:57: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:35:03: 1000000 INFO @ Fri, 10 Dec 2021 20:35:09: 2000000 INFO @ Fri, 10 Dec 2021 20:35:15: 3000000 INFO @ Fri, 10 Dec 2021 20:35:21: 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 20:35:27: 5000000 INFO @ Fri, 10 Dec 2021 20:35:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978880/ERX3978880.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978880/ERX3978880.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978880/ERX3978880.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978880/ERX3978880.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 20:35:27: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:35:27: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:35:33: 6000000 INFO @ Fri, 10 Dec 2021 20:35:35: 1000000 INFO @ Fri, 10 Dec 2021 20:35:40: 7000000 INFO @ Fri, 10 Dec 2021 20:35:43: 2000000 INFO @ Fri, 10 Dec 2021 20:35:48: 8000000 INFO @ Fri, 10 Dec 2021 20:35:51: 3000000 INFO @ Fri, 10 Dec 2021 20:35:55: 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 20:35:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978880/ERX3978880.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978880/ERX3978880.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978880/ERX3978880.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978880/ERX3978880.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 20:35:57: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:35:57: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:35:59: 4000000 INFO @ Fri, 10 Dec 2021 20:36:02: 10000000 INFO @ Fri, 10 Dec 2021 20:36:03: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 20:36:03: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 20:36:03: #1 total tags in treatment: 3897008 INFO @ Fri, 10 Dec 2021 20:36:03: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:36:03: #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 20:36:03: #1 tags after filtering in treatment: 3536189 INFO @ Fri, 10 Dec 2021 20:36:03: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 20:36:03: #1 finished! INFO @ Fri, 10 Dec 2021 20:36:03: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:36:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:36:04: #2 number of paired peaks: 6429 INFO @ Fri, 10 Dec 2021 20:36:04: start model_add_line... INFO @ Fri, 10 Dec 2021 20:36:04: start X-correlation... INFO @ Fri, 10 Dec 2021 20:36:04: end of X-cor INFO @ Fri, 10 Dec 2021 20:36:04: #2 finished! INFO @ Fri, 10 Dec 2021 20:36:04: #2 predicted fragment length is 230 bps INFO @ Fri, 10 Dec 2021 20:36:04: #2 alternative fragment length(s) may be 230 bps INFO @ Fri, 10 Dec 2021 20:36:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978880/ERX3978880.05_model.r INFO @ Fri, 10 Dec 2021 20:36:04: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:36:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:36:04: 1000000 INFO @ Fri, 10 Dec 2021 20:36:07: 5000000 INFO @ Fri, 10 Dec 2021 20:36:11: 2000000 INFO @ Fri, 10 Dec 2021 20:36:12: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:36:15: 6000000 INFO @ Fri, 10 Dec 2021 20:36:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978880/ERX3978880.05_peaks.xls INFO @ Fri, 10 Dec 2021 20:36:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978880/ERX3978880.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:36:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978880/ERX3978880.05_summits.bed INFO @ Fri, 10 Dec 2021 20:36:17: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7140 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 20:36:19: 3000000 INFO @ Fri, 10 Dec 2021 20:36:23: 7000000 INFO @ Fri, 10 Dec 2021 20:36:26: 4000000 INFO @ Fri, 10 Dec 2021 20:36:31: 8000000 INFO @ Fri, 10 Dec 2021 20:36:33: 5000000 INFO @ Fri, 10 Dec 2021 20:36:39: 9000000 INFO @ Fri, 10 Dec 2021 20:36:40: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 20:36:47: 10000000 INFO @ Fri, 10 Dec 2021 20:36:47: 7000000 INFO @ Fri, 10 Dec 2021 20:36:48: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 20:36:48: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 20:36:48: #1 total tags in treatment: 3897008 INFO @ Fri, 10 Dec 2021 20:36:48: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:36:48: #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 20:36:48: #1 tags after filtering in treatment: 3536189 INFO @ Fri, 10 Dec 2021 20:36:48: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 20:36:48: #1 finished! INFO @ Fri, 10 Dec 2021 20:36:48: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:36:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:36:49: #2 number of paired peaks: 6429 INFO @ Fri, 10 Dec 2021 20:36:49: start model_add_line... INFO @ Fri, 10 Dec 2021 20:36:49: start X-correlation... INFO @ Fri, 10 Dec 2021 20:36:49: end of X-cor INFO @ Fri, 10 Dec 2021 20:36:49: #2 finished! INFO @ Fri, 10 Dec 2021 20:36:49: #2 predicted fragment length is 230 bps INFO @ Fri, 10 Dec 2021 20:36:49: #2 alternative fragment length(s) may be 230 bps INFO @ Fri, 10 Dec 2021 20:36:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978880/ERX3978880.10_model.r INFO @ Fri, 10 Dec 2021 20:36:49: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:36:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:36:54: 8000000 INFO @ Fri, 10 Dec 2021 20:36:57: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 20:37:01: 9000000 INFO @ Fri, 10 Dec 2021 20:37:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978880/ERX3978880.10_peaks.xls INFO @ Fri, 10 Dec 2021 20:37:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978880/ERX3978880.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:37:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978880/ERX3978880.10_summits.bed INFO @ Fri, 10 Dec 2021 20:37:01: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5578 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 20:37:08: 10000000 INFO @ Fri, 10 Dec 2021 20:37:09: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 20:37:09: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 20:37:09: #1 total tags in treatment: 3897008 INFO @ Fri, 10 Dec 2021 20:37:09: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:37:09: #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 20:37:09: #1 tags after filtering in treatment: 3536189 INFO @ Fri, 10 Dec 2021 20:37:09: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 20:37:09: #1 finished! INFO @ Fri, 10 Dec 2021 20:37:09: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:37:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:37:09: #2 number of paired peaks: 6429 INFO @ Fri, 10 Dec 2021 20:37:09: start model_add_line... INFO @ Fri, 10 Dec 2021 20:37:09: start X-correlation... INFO @ Fri, 10 Dec 2021 20:37:09: end of X-cor INFO @ Fri, 10 Dec 2021 20:37:09: #2 finished! INFO @ Fri, 10 Dec 2021 20:37:09: #2 predicted fragment length is 230 bps INFO @ Fri, 10 Dec 2021 20:37:09: #2 alternative fragment length(s) may be 230 bps INFO @ Fri, 10 Dec 2021 20:37:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978880/ERX3978880.20_model.r INFO @ Fri, 10 Dec 2021 20:37:09: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:37:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:37:17: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:37:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978880/ERX3978880.20_peaks.xls INFO @ Fri, 10 Dec 2021 20:37:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978880/ERX3978880.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:37:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978880/ERX3978880.20_summits.bed INFO @ Fri, 10 Dec 2021 20:37:21: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3981 records, 4 fields): 5 millis CompletedMACS2peakCalling