Job ID = 16439343 SRX = SRX13453875 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9477756 spots for SRR17276263/SRR17276263.sra Written 9477756 spots for SRR17276263/SRR17276263.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439483 ("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: 00:18:57 9477756 reads; of these: 9477756 (100.00%) were paired; of these: 695107 (7.33%) aligned concordantly 0 times 6948950 (73.32%) aligned concordantly exactly 1 time 1833699 (19.35%) aligned concordantly >1 times ---- 695107 pairs aligned concordantly 0 times; of these: 248684 (35.78%) aligned discordantly 1 time ---- 446423 pairs aligned 0 times concordantly or discordantly; of these: 892846 mates make up the pairs; of these: 472501 (52.92%) aligned 0 times 210979 (23.63%) aligned exactly 1 time 209366 (23.45%) aligned >1 times 97.51% overall alignment rate Time searching: 00:18:57 Overall time: 00:18:57 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 8 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] 222788 / 8973424 = 0.0248 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:22:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13453875/SRX13453875.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13453875/SRX13453875.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13453875/SRX13453875.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13453875/SRX13453875.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 @ Tue, 02 Aug 2022 15:22:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:22:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:22:59: 1000000 INFO @ Tue, 02 Aug 2022 15:23:06: 2000000 INFO @ Tue, 02 Aug 2022 15:23:14: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:23:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13453875/SRX13453875.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13453875/SRX13453875.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13453875/SRX13453875.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13453875/SRX13453875.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 @ Tue, 02 Aug 2022 15:23:20: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:23:20: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:23:21: 4000000 INFO @ Tue, 02 Aug 2022 15:23:28: 1000000 INFO @ Tue, 02 Aug 2022 15:23:30: 5000000 INFO @ Tue, 02 Aug 2022 15:23:36: 2000000 INFO @ Tue, 02 Aug 2022 15:23:39: 6000000 INFO @ Tue, 02 Aug 2022 15:23:44: 3000000 INFO @ Tue, 02 Aug 2022 15:23:47: 7000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:23:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13453875/SRX13453875.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13453875/SRX13453875.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13453875/SRX13453875.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13453875/SRX13453875.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 @ Tue, 02 Aug 2022 15:23:50: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:23:50: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:23:52: 4000000 INFO @ Tue, 02 Aug 2022 15:23:56: 8000000 INFO @ Tue, 02 Aug 2022 15:23:58: 1000000 INFO @ Tue, 02 Aug 2022 15:24:01: 5000000 INFO @ Tue, 02 Aug 2022 15:24:04: 9000000 INFO @ Tue, 02 Aug 2022 15:24:06: 2000000 INFO @ Tue, 02 Aug 2022 15:24:09: 6000000 INFO @ Tue, 02 Aug 2022 15:24:13: 10000000 INFO @ Tue, 02 Aug 2022 15:24:14: 3000000 INFO @ Tue, 02 Aug 2022 15:24:18: 7000000 INFO @ Tue, 02 Aug 2022 15:24:22: 11000000 INFO @ Tue, 02 Aug 2022 15:24:23: 4000000 INFO @ Tue, 02 Aug 2022 15:24:26: 8000000 INFO @ Tue, 02 Aug 2022 15:24:31: 12000000 INFO @ Tue, 02 Aug 2022 15:24:31: 5000000 INFO @ Tue, 02 Aug 2022 15:24:34: 9000000 INFO @ Tue, 02 Aug 2022 15:24:39: 6000000 INFO @ Tue, 02 Aug 2022 15:24:39: 13000000 INFO @ Tue, 02 Aug 2022 15:24:42: 10000000 INFO @ Tue, 02 Aug 2022 15:24:47: 7000000 INFO @ Tue, 02 Aug 2022 15:24:48: 14000000 INFO @ Tue, 02 Aug 2022 15:24:51: 11000000 INFO @ Tue, 02 Aug 2022 15:24:56: 8000000 INFO @ Tue, 02 Aug 2022 15:24:57: 15000000 INFO @ Tue, 02 Aug 2022 15:24:59: 12000000 INFO @ Tue, 02 Aug 2022 15:25:04: 9000000 INFO @ Tue, 02 Aug 2022 15:25:06: 16000000 INFO @ Tue, 02 Aug 2022 15:25:07: 13000000 INFO @ Tue, 02 Aug 2022 15:25:12: 10000000 INFO @ Tue, 02 Aug 2022 15:25:15: 17000000 INFO @ Tue, 02 Aug 2022 15:25:16: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:25:20: 11000000 INFO @ Tue, 02 Aug 2022 15:25:23: 18000000 INFO @ Tue, 02 Aug 2022 15:25:23: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:25:23: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:25:23: #1 total tags in treatment: 8560663 INFO @ Tue, 02 Aug 2022 15:25:23: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:25:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:25:23: #1 tags after filtering in treatment: 8282378 INFO @ Tue, 02 Aug 2022 15:25:23: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:25:23: #1 finished! INFO @ Tue, 02 Aug 2022 15:25:23: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:25:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:25:24: #2 number of paired peaks: 180 WARNING @ Tue, 02 Aug 2022 15:25:24: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Tue, 02 Aug 2022 15:25:24: start model_add_line... INFO @ Tue, 02 Aug 2022 15:25:24: start X-correlation... INFO @ Tue, 02 Aug 2022 15:25:24: 15000000 INFO @ Tue, 02 Aug 2022 15:25:24: end of X-cor INFO @ Tue, 02 Aug 2022 15:25:24: #2 finished! INFO @ Tue, 02 Aug 2022 15:25:24: #2 predicted fragment length is 203 bps INFO @ Tue, 02 Aug 2022 15:25:24: #2 alternative fragment length(s) may be 203 bps INFO @ Tue, 02 Aug 2022 15:25:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13453875/SRX13453875.05_model.r INFO @ Tue, 02 Aug 2022 15:25:24: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:25:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:25:29: 12000000 INFO @ Tue, 02 Aug 2022 15:25:32: 16000000 INFO @ Tue, 02 Aug 2022 15:25:37: 13000000 INFO @ Tue, 02 Aug 2022 15:25:40: 17000000 INFO @ Tue, 02 Aug 2022 15:25:41: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:25:45: 14000000 INFO @ Tue, 02 Aug 2022 15:25:49: 18000000 INFO @ Tue, 02 Aug 2022 15:25:49: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:25:49: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:25:49: #1 total tags in treatment: 8560663 INFO @ Tue, 02 Aug 2022 15:25:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:25:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:25:49: #1 tags after filtering in treatment: 8282378 INFO @ Tue, 02 Aug 2022 15:25:49: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:25:49: #1 finished! INFO @ Tue, 02 Aug 2022 15:25:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:25:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:25:50: #2 number of paired peaks: 180 WARNING @ Tue, 02 Aug 2022 15:25:50: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Tue, 02 Aug 2022 15:25:50: start model_add_line... INFO @ Tue, 02 Aug 2022 15:25:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13453875/SRX13453875.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:25:50: start X-correlation... INFO @ Tue, 02 Aug 2022 15:25:50: end of X-cor INFO @ Tue, 02 Aug 2022 15:25:50: #2 finished! INFO @ Tue, 02 Aug 2022 15:25:50: #2 predicted fragment length is 203 bps INFO @ Tue, 02 Aug 2022 15:25:50: #2 alternative fragment length(s) may be 203 bps INFO @ Tue, 02 Aug 2022 15:25:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13453875/SRX13453875.10_model.r INFO @ Tue, 02 Aug 2022 15:25:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13453875/SRX13453875.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:25:50: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:25:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:25:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13453875/SRX13453875.05_summits.bed INFO @ Tue, 02 Aug 2022 15:25:50: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (2398 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:25:53: 15000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:26:01: 16000000 INFO @ Tue, 02 Aug 2022 15:26:07: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:26:09: 17000000 INFO @ Tue, 02 Aug 2022 15:26:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13453875/SRX13453875.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:26:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13453875/SRX13453875.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:26:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13453875/SRX13453875.10_summits.bed INFO @ Tue, 02 Aug 2022 15:26:16: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (1046 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:26:16: 18000000 INFO @ Tue, 02 Aug 2022 15:26:16: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:26:16: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:26:16: #1 total tags in treatment: 8560663 INFO @ Tue, 02 Aug 2022 15:26:16: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:26:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:26:16: #1 tags after filtering in treatment: 8282378 INFO @ Tue, 02 Aug 2022 15:26:16: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:26:16: #1 finished! INFO @ Tue, 02 Aug 2022 15:26:16: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:26:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:26:17: #2 number of paired peaks: 180 WARNING @ Tue, 02 Aug 2022 15:26:17: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Tue, 02 Aug 2022 15:26:17: start model_add_line... INFO @ Tue, 02 Aug 2022 15:26:17: start X-correlation... INFO @ Tue, 02 Aug 2022 15:26:17: end of X-cor INFO @ Tue, 02 Aug 2022 15:26:17: #2 finished! INFO @ Tue, 02 Aug 2022 15:26:17: #2 predicted fragment length is 203 bps INFO @ Tue, 02 Aug 2022 15:26:17: #2 alternative fragment length(s) may be 203 bps INFO @ Tue, 02 Aug 2022 15:26:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13453875/SRX13453875.20_model.r INFO @ Tue, 02 Aug 2022 15:26:17: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:26:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:26:35: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:26:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13453875/SRX13453875.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:26:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13453875/SRX13453875.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:26:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13453875/SRX13453875.20_summits.bed INFO @ Tue, 02 Aug 2022 15:26:43: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (470 records, 4 fields): 49 millis CompletedMACS2peakCalling