Job ID = 14168223 SRX = SRX7175253 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 33046954 spots for SRR10485693/SRR10485693.sra Written 33046954 spots for SRR10485693/SRR10485693.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169168 ("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: 00:45:14 33046954 reads; of these: 33046954 (100.00%) were paired; of these: 19292648 (58.38%) aligned concordantly 0 times 8017819 (24.26%) aligned concordantly exactly 1 time 5736487 (17.36%) aligned concordantly >1 times ---- 19292648 pairs aligned concordantly 0 times; of these: 133661 (0.69%) aligned discordantly 1 time ---- 19158987 pairs aligned 0 times concordantly or discordantly; of these: 38317974 mates make up the pairs; of these: 37455658 (97.75%) aligned 0 times 408130 (1.07%) aligned exactly 1 time 454186 (1.19%) aligned >1 times 43.33% overall alignment rate Time searching: 00:45:14 Overall time: 00:45:14 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] 4188836 / 13866612 = 0.3021 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 17:06:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7175253/SRX7175253.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7175253/SRX7175253.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7175253/SRX7175253.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7175253/SRX7175253.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 17:06:56: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:06:56: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:07:01: 1000000 INFO @ Fri, 10 Dec 2021 17:07:06: 2000000 INFO @ Fri, 10 Dec 2021 17:07:11: 3000000 INFO @ Fri, 10 Dec 2021 17:07:15: 4000000 INFO @ Fri, 10 Dec 2021 17:07:20: 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 17:07:25: 6000000 INFO @ Fri, 10 Dec 2021 17:07:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7175253/SRX7175253.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7175253/SRX7175253.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7175253/SRX7175253.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7175253/SRX7175253.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 17:07:26: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:07:26: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:07:30: 7000000 INFO @ Fri, 10 Dec 2021 17:07:32: 1000000 INFO @ Fri, 10 Dec 2021 17:07:35: 8000000 INFO @ Fri, 10 Dec 2021 17:07:38: 2000000 INFO @ Fri, 10 Dec 2021 17:07:40: 9000000 INFO @ Fri, 10 Dec 2021 17:07:44: 3000000 INFO @ Fri, 10 Dec 2021 17:07:44: 10000000 INFO @ Fri, 10 Dec 2021 17:07:49: 11000000 INFO @ Fri, 10 Dec 2021 17:07:50: 4000000 INFO @ Fri, 10 Dec 2021 17:07:54: 12000000 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 17:07:56: 5000000 INFO @ Fri, 10 Dec 2021 17:07:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7175253/SRX7175253.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7175253/SRX7175253.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7175253/SRX7175253.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7175253/SRX7175253.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 17:07:56: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:07:56: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:07:59: 13000000 INFO @ Fri, 10 Dec 2021 17:08:02: 6000000 INFO @ Fri, 10 Dec 2021 17:08:02: 1000000 INFO @ Fri, 10 Dec 2021 17:08:04: 14000000 INFO @ Fri, 10 Dec 2021 17:08:08: 7000000 INFO @ Fri, 10 Dec 2021 17:08:08: 2000000 INFO @ Fri, 10 Dec 2021 17:08:09: 15000000 INFO @ Fri, 10 Dec 2021 17:08:14: 16000000 INFO @ Fri, 10 Dec 2021 17:08:14: 8000000 INFO @ Fri, 10 Dec 2021 17:08:14: 3000000 INFO @ Fri, 10 Dec 2021 17:08:19: 17000000 INFO @ Fri, 10 Dec 2021 17:08:20: 9000000 INFO @ Fri, 10 Dec 2021 17:08:20: 4000000 INFO @ Fri, 10 Dec 2021 17:08:24: 18000000 INFO @ Fri, 10 Dec 2021 17:08:26: 10000000 INFO @ Fri, 10 Dec 2021 17:08:26: 5000000 INFO @ Fri, 10 Dec 2021 17:08:29: 19000000 INFO @ Fri, 10 Dec 2021 17:08:32: 11000000 INFO @ Fri, 10 Dec 2021 17:08:32: 6000000 INFO @ Fri, 10 Dec 2021 17:08:34: 20000000 INFO @ Fri, 10 Dec 2021 17:08:35: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 17:08:35: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 17:08:35: #1 total tags in treatment: 9594630 INFO @ Fri, 10 Dec 2021 17:08:35: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:08:35: #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 17:08:35: #1 tags after filtering in treatment: 8660799 INFO @ Fri, 10 Dec 2021 17:08:35: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 10 Dec 2021 17:08:35: #1 finished! INFO @ Fri, 10 Dec 2021 17:08:35: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:08:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:08:36: #2 number of paired peaks: 787 WARNING @ Fri, 10 Dec 2021 17:08:36: Fewer paired peaks (787) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 787 pairs to build model! INFO @ Fri, 10 Dec 2021 17:08:36: start model_add_line... INFO @ Fri, 10 Dec 2021 17:08:36: start X-correlation... INFO @ Fri, 10 Dec 2021 17:08:36: end of X-cor INFO @ Fri, 10 Dec 2021 17:08:36: #2 finished! INFO @ Fri, 10 Dec 2021 17:08:36: #2 predicted fragment length is 170 bps INFO @ Fri, 10 Dec 2021 17:08:36: #2 alternative fragment length(s) may be 170 bps INFO @ Fri, 10 Dec 2021 17:08:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7175253/SRX7175253.05_model.r INFO @ Fri, 10 Dec 2021 17:08:36: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:08:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:08:38: 12000000 INFO @ Fri, 10 Dec 2021 17:08:38: 7000000 INFO @ Fri, 10 Dec 2021 17:08:44: 13000000 INFO @ Fri, 10 Dec 2021 17:08:44: 8000000 INFO @ Fri, 10 Dec 2021 17:08:50: 14000000 INFO @ Fri, 10 Dec 2021 17:08:50: 9000000 INFO @ Fri, 10 Dec 2021 17:08:54: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:08:56: 15000000 INFO @ Fri, 10 Dec 2021 17:08:56: 10000000 INFO @ Fri, 10 Dec 2021 17:09:02: 16000000 INFO @ Fri, 10 Dec 2021 17:09:02: 11000000 INFO @ Fri, 10 Dec 2021 17:09:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7175253/SRX7175253.05_peaks.xls INFO @ Fri, 10 Dec 2021 17:09:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7175253/SRX7175253.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:09:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7175253/SRX7175253.05_summits.bed INFO @ Fri, 10 Dec 2021 17:09:03: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6294 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:09:08: 17000000 INFO @ Fri, 10 Dec 2021 17:09:08: 12000000 INFO @ Fri, 10 Dec 2021 17:09:14: 18000000 INFO @ Fri, 10 Dec 2021 17:09:14: 13000000 INFO @ Fri, 10 Dec 2021 17:09:20: 19000000 INFO @ Fri, 10 Dec 2021 17:09:20: 14000000 INFO @ Fri, 10 Dec 2021 17:09:26: 15000000 INFO @ Fri, 10 Dec 2021 17:09:26: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 17:09:28: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 17:09:28: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 17:09:28: #1 total tags in treatment: 9594630 INFO @ Fri, 10 Dec 2021 17:09:28: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:09:28: #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 17:09:28: #1 tags after filtering in treatment: 8660799 INFO @ Fri, 10 Dec 2021 17:09:28: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 10 Dec 2021 17:09:28: #1 finished! INFO @ Fri, 10 Dec 2021 17:09:28: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:09:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:09:28: #2 number of paired peaks: 787 WARNING @ Fri, 10 Dec 2021 17:09:28: Fewer paired peaks (787) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 787 pairs to build model! INFO @ Fri, 10 Dec 2021 17:09:28: start model_add_line... INFO @ Fri, 10 Dec 2021 17:09:28: start X-correlation... INFO @ Fri, 10 Dec 2021 17:09:28: end of X-cor INFO @ Fri, 10 Dec 2021 17:09:28: #2 finished! INFO @ Fri, 10 Dec 2021 17:09:28: #2 predicted fragment length is 170 bps INFO @ Fri, 10 Dec 2021 17:09:28: #2 alternative fragment length(s) may be 170 bps INFO @ Fri, 10 Dec 2021 17:09:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7175253/SRX7175253.10_model.r INFO @ Fri, 10 Dec 2021 17:09:28: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:09:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:09:32: 16000000 INFO @ Fri, 10 Dec 2021 17:09:38: 17000000 INFO @ Fri, 10 Dec 2021 17:09:44: 18000000 INFO @ Fri, 10 Dec 2021 17:09:46: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:09:49: 19000000 INFO @ Fri, 10 Dec 2021 17:09:55: 20000000 INFO @ Fri, 10 Dec 2021 17:09:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7175253/SRX7175253.10_peaks.xls INFO @ Fri, 10 Dec 2021 17:09:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7175253/SRX7175253.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:09:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7175253/SRX7175253.10_summits.bed INFO @ Fri, 10 Dec 2021 17:09:55: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3105 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:09:57: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 17:09:57: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 17:09:57: #1 total tags in treatment: 9594630 INFO @ Fri, 10 Dec 2021 17:09:57: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:09:57: #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 17:09:57: #1 tags after filtering in treatment: 8660799 INFO @ Fri, 10 Dec 2021 17:09:57: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 10 Dec 2021 17:09:57: #1 finished! INFO @ Fri, 10 Dec 2021 17:09:57: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:09:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:09:58: #2 number of paired peaks: 787 WARNING @ Fri, 10 Dec 2021 17:09:58: Fewer paired peaks (787) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 787 pairs to build model! INFO @ Fri, 10 Dec 2021 17:09:58: start model_add_line... INFO @ Fri, 10 Dec 2021 17:09:58: start X-correlation... INFO @ Fri, 10 Dec 2021 17:09:58: end of X-cor INFO @ Fri, 10 Dec 2021 17:09:58: #2 finished! INFO @ Fri, 10 Dec 2021 17:09:58: #2 predicted fragment length is 170 bps INFO @ Fri, 10 Dec 2021 17:09:58: #2 alternative fragment length(s) may be 170 bps INFO @ Fri, 10 Dec 2021 17:09:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7175253/SRX7175253.20_model.r INFO @ Fri, 10 Dec 2021 17:09:58: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:09:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 17:10:16: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:10:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7175253/SRX7175253.20_peaks.xls INFO @ Fri, 10 Dec 2021 17:10:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7175253/SRX7175253.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:10:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7175253/SRX7175253.20_summits.bed INFO @ Fri, 10 Dec 2021 17:10:25: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1269 records, 4 fields): 2 millis CompletedMACS2peakCalling