Job ID = 14172167 SRX = SRX9786721 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13052549 spots for SRR13362640/SRR13362640.sra Written 13052549 spots for SRR13362640/SRR13362640.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172680 ("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: 00:15:13 13052549 reads; of these: 13052549 (100.00%) were paired; of these: 3832631 (29.36%) aligned concordantly 0 times 6125748 (46.93%) aligned concordantly exactly 1 time 3094170 (23.71%) aligned concordantly >1 times ---- 3832631 pairs aligned concordantly 0 times; of these: 808344 (21.09%) aligned discordantly 1 time ---- 3024287 pairs aligned 0 times concordantly or discordantly; of these: 6048574 mates make up the pairs; of these: 5149671 (85.14%) aligned 0 times 396055 (6.55%) aligned exactly 1 time 502848 (8.31%) aligned >1 times 80.27% overall alignment rate Time searching: 00:15:13 Overall time: 00:15:13 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] 1174200 / 9944568 = 0.1181 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 @ Sat, 11 Dec 2021 14:58:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9786721/SRX9786721.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9786721/SRX9786721.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9786721/SRX9786721.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9786721/SRX9786721.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 @ Sat, 11 Dec 2021 14:58:19: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:58:19: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:58:24: 1000000 INFO @ Sat, 11 Dec 2021 14:58:29: 2000000 INFO @ Sat, 11 Dec 2021 14:58:34: 3000000 INFO @ Sat, 11 Dec 2021 14:58:38: 4000000 INFO @ Sat, 11 Dec 2021 14:58:43: 5000000 INFO @ Sat, 11 Dec 2021 14:58:48: 6000000 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 @ Sat, 11 Dec 2021 14:58:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9786721/SRX9786721.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9786721/SRX9786721.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9786721/SRX9786721.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9786721/SRX9786721.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 @ Sat, 11 Dec 2021 14:58:50: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:58:50: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:58:53: 7000000 INFO @ Sat, 11 Dec 2021 14:58:56: 1000000 INFO @ Sat, 11 Dec 2021 14:58:58: 8000000 INFO @ Sat, 11 Dec 2021 14:59:02: 2000000 INFO @ Sat, 11 Dec 2021 14:59:03: 9000000 INFO @ Sat, 11 Dec 2021 14:59:08: 3000000 INFO @ Sat, 11 Dec 2021 14:59:09: 10000000 INFO @ Sat, 11 Dec 2021 14:59:14: 11000000 INFO @ Sat, 11 Dec 2021 14:59:14: 4000000 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 @ Sat, 11 Dec 2021 14:59:19: 12000000 INFO @ Sat, 11 Dec 2021 14:59:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9786721/SRX9786721.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9786721/SRX9786721.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9786721/SRX9786721.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9786721/SRX9786721.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 @ Sat, 11 Dec 2021 14:59:19: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:59:19: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:59:21: 5000000 INFO @ Sat, 11 Dec 2021 14:59:24: 13000000 INFO @ Sat, 11 Dec 2021 14:59:25: 1000000 INFO @ Sat, 11 Dec 2021 14:59:27: 6000000 INFO @ Sat, 11 Dec 2021 14:59:29: 14000000 INFO @ Sat, 11 Dec 2021 14:59:30: 2000000 INFO @ Sat, 11 Dec 2021 14:59:33: 7000000 INFO @ Sat, 11 Dec 2021 14:59:35: 15000000 INFO @ Sat, 11 Dec 2021 14:59:35: 3000000 INFO @ Sat, 11 Dec 2021 14:59:40: 8000000 INFO @ Sat, 11 Dec 2021 14:59:40: 16000000 INFO @ Sat, 11 Dec 2021 14:59:41: 4000000 INFO @ Sat, 11 Dec 2021 14:59:46: 17000000 INFO @ Sat, 11 Dec 2021 14:59:46: 9000000 INFO @ Sat, 11 Dec 2021 14:59:46: 5000000 INFO @ Sat, 11 Dec 2021 14:59:51: 18000000 INFO @ Sat, 11 Dec 2021 14:59:51: 6000000 INFO @ Sat, 11 Dec 2021 14:59:52: 10000000 INFO @ Sat, 11 Dec 2021 14:59:54: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 14:59:54: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 14:59:54: #1 total tags in treatment: 8061512 INFO @ Sat, 11 Dec 2021 14:59:54: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:59:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 14:59:55: #1 tags after filtering in treatment: 6940319 INFO @ Sat, 11 Dec 2021 14:59:55: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 11 Dec 2021 14:59:55: #1 finished! INFO @ Sat, 11 Dec 2021 14:59:55: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:59:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:59:55: #2 number of paired peaks: 197 WARNING @ Sat, 11 Dec 2021 14:59:55: Fewer paired peaks (197) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 197 pairs to build model! INFO @ Sat, 11 Dec 2021 14:59:55: start model_add_line... INFO @ Sat, 11 Dec 2021 14:59:55: start X-correlation... INFO @ Sat, 11 Dec 2021 14:59:55: end of X-cor INFO @ Sat, 11 Dec 2021 14:59:55: #2 finished! INFO @ Sat, 11 Dec 2021 14:59:55: #2 predicted fragment length is 107 bps INFO @ Sat, 11 Dec 2021 14:59:55: #2 alternative fragment length(s) may be 107 bps INFO @ Sat, 11 Dec 2021 14:59:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9786721/SRX9786721.05_model.r INFO @ Sat, 11 Dec 2021 14:59:55: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:59:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:59:57: 7000000 INFO @ Sat, 11 Dec 2021 14:59:58: 11000000 INFO @ Sat, 11 Dec 2021 15:00:02: 8000000 INFO @ Sat, 11 Dec 2021 15:00:04: 12000000 INFO @ Sat, 11 Dec 2021 15:00:07: 9000000 INFO @ Sat, 11 Dec 2021 15:00:10: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:00:11: 13000000 INFO @ Sat, 11 Dec 2021 15:00:13: 10000000 INFO @ Sat, 11 Dec 2021 15:00:17: 14000000 INFO @ Sat, 11 Dec 2021 15:00:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9786721/SRX9786721.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:00:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9786721/SRX9786721.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:00:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9786721/SRX9786721.05_summits.bed INFO @ Sat, 11 Dec 2021 15:00:17: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2480 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:00:18: 11000000 INFO @ Sat, 11 Dec 2021 15:00:23: 15000000 INFO @ Sat, 11 Dec 2021 15:00:23: 12000000 INFO @ Sat, 11 Dec 2021 15:00:29: 13000000 INFO @ Sat, 11 Dec 2021 15:00:29: 16000000 INFO @ Sat, 11 Dec 2021 15:00:34: 14000000 INFO @ Sat, 11 Dec 2021 15:00:35: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:00:39: 15000000 INFO @ Sat, 11 Dec 2021 15:00:41: 18000000 INFO @ Sat, 11 Dec 2021 15:00:44: 16000000 INFO @ Sat, 11 Dec 2021 15:00:45: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 15:00:45: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 15:00:45: #1 total tags in treatment: 8061512 INFO @ Sat, 11 Dec 2021 15:00:45: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:00:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:00:45: #1 tags after filtering in treatment: 6940319 INFO @ Sat, 11 Dec 2021 15:00:45: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 11 Dec 2021 15:00:45: #1 finished! INFO @ Sat, 11 Dec 2021 15:00:45: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:00:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:00:46: #2 number of paired peaks: 197 WARNING @ Sat, 11 Dec 2021 15:00:46: Fewer paired peaks (197) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 197 pairs to build model! INFO @ Sat, 11 Dec 2021 15:00:46: start model_add_line... INFO @ Sat, 11 Dec 2021 15:00:46: start X-correlation... INFO @ Sat, 11 Dec 2021 15:00:46: end of X-cor INFO @ Sat, 11 Dec 2021 15:00:46: #2 finished! INFO @ Sat, 11 Dec 2021 15:00:46: #2 predicted fragment length is 107 bps INFO @ Sat, 11 Dec 2021 15:00:46: #2 alternative fragment length(s) may be 107 bps INFO @ Sat, 11 Dec 2021 15:00:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9786721/SRX9786721.10_model.r INFO @ Sat, 11 Dec 2021 15:00:46: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:00:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:00:49: 17000000 INFO @ Sat, 11 Dec 2021 15:00:54: 18000000 INFO @ Sat, 11 Dec 2021 15:00:57: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 15:00:57: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 15:00:57: #1 total tags in treatment: 8061512 INFO @ Sat, 11 Dec 2021 15:00:57: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:00:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:00:58: #1 tags after filtering in treatment: 6940319 INFO @ Sat, 11 Dec 2021 15:00:58: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 11 Dec 2021 15:00:58: #1 finished! INFO @ Sat, 11 Dec 2021 15:00:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:00:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:00:58: #2 number of paired peaks: 197 WARNING @ Sat, 11 Dec 2021 15:00:58: Fewer paired peaks (197) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 197 pairs to build model! INFO @ Sat, 11 Dec 2021 15:00:58: start model_add_line... INFO @ Sat, 11 Dec 2021 15:00:58: start X-correlation... INFO @ Sat, 11 Dec 2021 15:00:58: end of X-cor INFO @ Sat, 11 Dec 2021 15:00:58: #2 finished! INFO @ Sat, 11 Dec 2021 15:00:58: #2 predicted fragment length is 107 bps INFO @ Sat, 11 Dec 2021 15:00:58: #2 alternative fragment length(s) may be 107 bps INFO @ Sat, 11 Dec 2021 15:00:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9786721/SRX9786721.20_model.r INFO @ Sat, 11 Dec 2021 15:00:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:00:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:01:00: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:01:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9786721/SRX9786721.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:01:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9786721/SRX9786721.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:01:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9786721/SRX9786721.10_summits.bed INFO @ Sat, 11 Dec 2021 15:01:08: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (888 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:01:12: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:01:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9786721/SRX9786721.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:01:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9786721/SRX9786721.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:01:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9786721/SRX9786721.20_summits.bed INFO @ Sat, 11 Dec 2021 15:01:19: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (283 records, 4 fields): 1 millis CompletedMACS2peakCalling