Job ID = 14167224 SRX = SRX8973507 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13730737 spots for SRR12479622/SRR12479622.sra Written 13730737 spots for SRR12479622/SRR12479622.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167860 ("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: 00:17:54 13730737 reads; of these: 13730737 (100.00%) were paired; of these: 6522010 (47.50%) aligned concordantly 0 times 5133785 (37.39%) aligned concordantly exactly 1 time 2074942 (15.11%) aligned concordantly >1 times ---- 6522010 pairs aligned concordantly 0 times; of these: 102790 (1.58%) aligned discordantly 1 time ---- 6419220 pairs aligned 0 times concordantly or discordantly; of these: 12838440 mates make up the pairs; of these: 12042752 (93.80%) aligned 0 times 494393 (3.85%) aligned exactly 1 time 301295 (2.35%) aligned >1 times 56.15% overall alignment rate Time searching: 00:17:54 Overall time: 00:17:54 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] 179557 / 7306606 = 0.0246 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 11:29:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8973507/SRX8973507.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8973507/SRX8973507.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8973507/SRX8973507.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8973507/SRX8973507.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 11:29:50: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:29:50: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:29:55: 1000000 INFO @ Fri, 10 Dec 2021 11:29:59: 2000000 INFO @ Fri, 10 Dec 2021 11:30:04: 3000000 INFO @ Fri, 10 Dec 2021 11:30:09: 4000000 INFO @ Fri, 10 Dec 2021 11:30:14: 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 11:30:19: 6000000 INFO @ Fri, 10 Dec 2021 11:30:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8973507/SRX8973507.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8973507/SRX8973507.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8973507/SRX8973507.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8973507/SRX8973507.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 11:30:19: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:30:19: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:30:24: 7000000 INFO @ Fri, 10 Dec 2021 11:30:25: 1000000 INFO @ Fri, 10 Dec 2021 11:30:29: 8000000 INFO @ Fri, 10 Dec 2021 11:30:30: 2000000 INFO @ Fri, 10 Dec 2021 11:30:34: 9000000 INFO @ Fri, 10 Dec 2021 11:30:35: 3000000 INFO @ Fri, 10 Dec 2021 11:30:39: 10000000 INFO @ Fri, 10 Dec 2021 11:30:40: 4000000 INFO @ Fri, 10 Dec 2021 11:30:44: 11000000 INFO @ Fri, 10 Dec 2021 11:30:46: 5000000 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 11:30:49: 12000000 INFO @ Fri, 10 Dec 2021 11:30:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8973507/SRX8973507.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8973507/SRX8973507.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8973507/SRX8973507.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8973507/SRX8973507.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 11:30:49: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:30:49: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:30:51: 6000000 INFO @ Fri, 10 Dec 2021 11:30:54: 13000000 INFO @ Fri, 10 Dec 2021 11:30:54: 1000000 INFO @ Fri, 10 Dec 2021 11:30:56: 7000000 INFO @ Fri, 10 Dec 2021 11:30:59: 14000000 INFO @ Fri, 10 Dec 2021 11:30:59: 2000000 INFO @ Fri, 10 Dec 2021 11:31:01: 8000000 INFO @ Fri, 10 Dec 2021 11:31:04: 15000000 INFO @ Fri, 10 Dec 2021 11:31:04: 3000000 INFO @ Fri, 10 Dec 2021 11:31:04: #1 tag size is determined as 42 bps INFO @ Fri, 10 Dec 2021 11:31:04: #1 tag size = 42 INFO @ Fri, 10 Dec 2021 11:31:04: #1 total tags in treatment: 7030156 INFO @ Fri, 10 Dec 2021 11:31:04: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:31:04: #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 11:31:04: #1 tags after filtering in treatment: 6815346 INFO @ Fri, 10 Dec 2021 11:31:04: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 10 Dec 2021 11:31:04: #1 finished! INFO @ Fri, 10 Dec 2021 11:31:04: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:31:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:31:05: #2 number of paired peaks: 209 WARNING @ Fri, 10 Dec 2021 11:31:05: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Fri, 10 Dec 2021 11:31:05: start model_add_line... INFO @ Fri, 10 Dec 2021 11:31:05: start X-correlation... INFO @ Fri, 10 Dec 2021 11:31:05: end of X-cor INFO @ Fri, 10 Dec 2021 11:31:05: #2 finished! INFO @ Fri, 10 Dec 2021 11:31:05: #2 predicted fragment length is 150 bps INFO @ Fri, 10 Dec 2021 11:31:05: #2 alternative fragment length(s) may be 150 bps INFO @ Fri, 10 Dec 2021 11:31:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8973507/SRX8973507.05_model.r INFO @ Fri, 10 Dec 2021 11:31:05: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:31:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:31:06: 9000000 INFO @ Fri, 10 Dec 2021 11:31:09: 4000000 INFO @ Fri, 10 Dec 2021 11:31:11: 10000000 INFO @ Fri, 10 Dec 2021 11:31:14: 5000000 INFO @ Fri, 10 Dec 2021 11:31:16: 11000000 INFO @ Fri, 10 Dec 2021 11:31:18: 6000000 INFO @ Fri, 10 Dec 2021 11:31:21: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:31:21: 12000000 INFO @ Fri, 10 Dec 2021 11:31:23: 7000000 INFO @ Fri, 10 Dec 2021 11:31:27: 13000000 INFO @ Fri, 10 Dec 2021 11:31:28: 8000000 INFO @ Fri, 10 Dec 2021 11:31:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8973507/SRX8973507.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:31:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8973507/SRX8973507.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:31:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8973507/SRX8973507.05_summits.bed INFO @ Fri, 10 Dec 2021 11:31:29: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (907 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:31:32: 14000000 INFO @ Fri, 10 Dec 2021 11:31:34: 9000000 INFO @ Fri, 10 Dec 2021 11:31:38: 15000000 INFO @ Fri, 10 Dec 2021 11:31:38: #1 tag size is determined as 42 bps INFO @ Fri, 10 Dec 2021 11:31:38: #1 tag size = 42 INFO @ Fri, 10 Dec 2021 11:31:38: #1 total tags in treatment: 7030156 INFO @ Fri, 10 Dec 2021 11:31:38: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:31:38: #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 11:31:38: #1 tags after filtering in treatment: 6815346 INFO @ Fri, 10 Dec 2021 11:31:38: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 10 Dec 2021 11:31:38: #1 finished! INFO @ Fri, 10 Dec 2021 11:31:38: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:31:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:31:39: 10000000 INFO @ Fri, 10 Dec 2021 11:31:39: #2 number of paired peaks: 209 WARNING @ Fri, 10 Dec 2021 11:31:39: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Fri, 10 Dec 2021 11:31:39: start model_add_line... INFO @ Fri, 10 Dec 2021 11:31:39: start X-correlation... INFO @ Fri, 10 Dec 2021 11:31:39: end of X-cor INFO @ Fri, 10 Dec 2021 11:31:39: #2 finished! INFO @ Fri, 10 Dec 2021 11:31:39: #2 predicted fragment length is 150 bps INFO @ Fri, 10 Dec 2021 11:31:39: #2 alternative fragment length(s) may be 150 bps INFO @ Fri, 10 Dec 2021 11:31:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8973507/SRX8973507.10_model.r INFO @ Fri, 10 Dec 2021 11:31:39: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:31:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:31:44: 11000000 INFO @ Fri, 10 Dec 2021 11:31:49: 12000000 INFO @ Fri, 10 Dec 2021 11:31:54: 13000000 INFO @ Fri, 10 Dec 2021 11:31:55: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:31:58: 14000000 INFO @ Fri, 10 Dec 2021 11:32:03: 15000000 INFO @ Fri, 10 Dec 2021 11:32:04: #1 tag size is determined as 42 bps INFO @ Fri, 10 Dec 2021 11:32:04: #1 tag size = 42 INFO @ Fri, 10 Dec 2021 11:32:04: #1 total tags in treatment: 7030156 INFO @ Fri, 10 Dec 2021 11:32:04: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:32:04: #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 11:32:04: #1 tags after filtering in treatment: 6815346 INFO @ Fri, 10 Dec 2021 11:32:04: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 10 Dec 2021 11:32:04: #1 finished! INFO @ Fri, 10 Dec 2021 11:32:04: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:32:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:32:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8973507/SRX8973507.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:32:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8973507/SRX8973507.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:32:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8973507/SRX8973507.10_summits.bed INFO @ Fri, 10 Dec 2021 11:32:04: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (586 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:32:04: #2 number of paired peaks: 209 WARNING @ Fri, 10 Dec 2021 11:32:04: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Fri, 10 Dec 2021 11:32:04: start model_add_line... INFO @ Fri, 10 Dec 2021 11:32:04: start X-correlation... INFO @ Fri, 10 Dec 2021 11:32:04: end of X-cor INFO @ Fri, 10 Dec 2021 11:32:04: #2 finished! INFO @ Fri, 10 Dec 2021 11:32:04: #2 predicted fragment length is 150 bps INFO @ Fri, 10 Dec 2021 11:32:04: #2 alternative fragment length(s) may be 150 bps INFO @ Fri, 10 Dec 2021 11:32:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8973507/SRX8973507.20_model.r INFO @ Fri, 10 Dec 2021 11:32:04: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:32:04: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:32:20: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:32:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8973507/SRX8973507.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:32:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8973507/SRX8973507.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:32:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8973507/SRX8973507.20_summits.bed INFO @ Fri, 10 Dec 2021 11:32:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (358 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。