Job ID = 14168360 SRX = SRX11078126 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-10T09:07:35 prefetch.2.10.7: 1) Downloading 'SRR14743554'... 2021-12-10T09:07:35 prefetch.2.10.7: Downloading via HTTPS... 2021-12-10T09:07:48 prefetch.2.10.7: HTTPS download succeed 2021-12-10T09:07:48 prefetch.2.10.7: 'SRR14743554' is valid 2021-12-10T09:07:48 prefetch.2.10.7: 1) 'SRR14743554' was downloaded successfully 2021-12-10T09:07:48 prefetch.2.10.7: 'SRR14743554' has 0 unresolved dependencies Read 6023466 spots for SRR14743554/SRR14743554.sra Written 6023466 spots for SRR14743554/SRR14743554.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169526 ("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: 00:01:10 6023466 reads; of these: 6023466 (100.00%) were paired; of these: 5765802 (95.72%) aligned concordantly 0 times 190577 (3.16%) aligned concordantly exactly 1 time 67087 (1.11%) aligned concordantly >1 times ---- 5765802 pairs aligned concordantly 0 times; of these: 224 (0.00%) aligned discordantly 1 time ---- 5765578 pairs aligned 0 times concordantly or discordantly; of these: 11531156 mates make up the pairs; of these: 11488837 (99.63%) aligned 0 times 12213 (0.11%) aligned exactly 1 time 30106 (0.26%) aligned >1 times 4.63% overall alignment rate Time searching: 00:01:10 Overall time: 00:01:10 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_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] 5396 / 257735 = 0.0209 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 18:10:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11078126/SRX11078126.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11078126/SRX11078126.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11078126/SRX11078126.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11078126/SRX11078126.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 18:10:06: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:10:06: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:10:09: #1 tag size is determined as 40 bps INFO @ Fri, 10 Dec 2021 18:10:09: #1 tag size = 40 INFO @ Fri, 10 Dec 2021 18:10:09: #1 total tags in treatment: 252269 INFO @ Fri, 10 Dec 2021 18:10:09: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:10:09: #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 18:10:09: #1 tags after filtering in treatment: 249815 INFO @ Fri, 10 Dec 2021 18:10:09: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 10 Dec 2021 18:10:09: #1 finished! INFO @ Fri, 10 Dec 2021 18:10:09: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:10:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:10:09: #2 number of paired peaks: 1075 INFO @ Fri, 10 Dec 2021 18:10:09: start model_add_line... INFO @ Fri, 10 Dec 2021 18:10:09: start X-correlation... INFO @ Fri, 10 Dec 2021 18:10:09: end of X-cor INFO @ Fri, 10 Dec 2021 18:10:09: #2 finished! INFO @ Fri, 10 Dec 2021 18:10:09: #2 predicted fragment length is 108 bps INFO @ Fri, 10 Dec 2021 18:10:09: #2 alternative fragment length(s) may be 98,108,216,586 bps INFO @ Fri, 10 Dec 2021 18:10:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11078126/SRX11078126.05_model.r INFO @ Fri, 10 Dec 2021 18:10:09: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:10:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:10:09: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:10:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11078126/SRX11078126.05_peaks.xls INFO @ Fri, 10 Dec 2021 18:10:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11078126/SRX11078126.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:10:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11078126/SRX11078126.05_summits.bed INFO @ Fri, 10 Dec 2021 18:10:10: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (57 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 18:10:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11078126/SRX11078126.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11078126/SRX11078126.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11078126/SRX11078126.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11078126/SRX11078126.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 18:10:36: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:10:36: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:10:39: #1 tag size is determined as 40 bps INFO @ Fri, 10 Dec 2021 18:10:39: #1 tag size = 40 INFO @ Fri, 10 Dec 2021 18:10:39: #1 total tags in treatment: 252269 INFO @ Fri, 10 Dec 2021 18:10:39: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:10:39: #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 18:10:39: #1 tags after filtering in treatment: 249815 INFO @ Fri, 10 Dec 2021 18:10:39: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 10 Dec 2021 18:10:39: #1 finished! INFO @ Fri, 10 Dec 2021 18:10:39: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:10:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:10:39: #2 number of paired peaks: 1075 INFO @ Fri, 10 Dec 2021 18:10:39: start model_add_line... INFO @ Fri, 10 Dec 2021 18:10:39: start X-correlation... INFO @ Fri, 10 Dec 2021 18:10:39: end of X-cor INFO @ Fri, 10 Dec 2021 18:10:39: #2 finished! INFO @ Fri, 10 Dec 2021 18:10:39: #2 predicted fragment length is 108 bps INFO @ Fri, 10 Dec 2021 18:10:39: #2 alternative fragment length(s) may be 98,108,216,586 bps INFO @ Fri, 10 Dec 2021 18:10:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11078126/SRX11078126.10_model.r INFO @ Fri, 10 Dec 2021 18:10:39: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:10:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:10:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:10:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11078126/SRX11078126.10_peaks.xls INFO @ Fri, 10 Dec 2021 18:10:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11078126/SRX11078126.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:10:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11078126/SRX11078126.10_summits.bed INFO @ Fri, 10 Dec 2021 18:10:40: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (37 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 18:11:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11078126/SRX11078126.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11078126/SRX11078126.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11078126/SRX11078126.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11078126/SRX11078126.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 18:11:06: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:11:06: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 18:11:09: #1 tag size is determined as 40 bps INFO @ Fri, 10 Dec 2021 18:11:09: #1 tag size = 40 INFO @ Fri, 10 Dec 2021 18:11:09: #1 total tags in treatment: 252269 INFO @ Fri, 10 Dec 2021 18:11:09: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:11:09: #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 18:11:09: #1 tags after filtering in treatment: 249815 INFO @ Fri, 10 Dec 2021 18:11:09: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 10 Dec 2021 18:11:09: #1 finished! INFO @ Fri, 10 Dec 2021 18:11:09: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:11:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:11:09: #2 number of paired peaks: 1075 INFO @ Fri, 10 Dec 2021 18:11:09: start model_add_line... INFO @ Fri, 10 Dec 2021 18:11:09: start X-correlation... INFO @ Fri, 10 Dec 2021 18:11:09: end of X-cor INFO @ Fri, 10 Dec 2021 18:11:09: #2 finished! INFO @ Fri, 10 Dec 2021 18:11:09: #2 predicted fragment length is 108 bps INFO @ Fri, 10 Dec 2021 18:11:09: #2 alternative fragment length(s) may be 98,108,216,586 bps INFO @ Fri, 10 Dec 2021 18:11:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11078126/SRX11078126.20_model.r INFO @ Fri, 10 Dec 2021 18:11:09: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:11:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:11:09: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:11:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11078126/SRX11078126.20_peaks.xls INFO @ Fri, 10 Dec 2021 18:11:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11078126/SRX11078126.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:11:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11078126/SRX11078126.20_summits.bed INFO @ Fri, 10 Dec 2021 18:11:10: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (22 records, 4 fields): 1 millis CompletedMACS2peakCalling