Job ID = 14172179 SRX = SRX9281729 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9681623 spots for SRR12813205/SRR12813205.sra Written 9681623 spots for SRR12813205/SRR12813205.sra Read 9520388 spots for SRR12813206/SRR12813206.sra Written 9520388 spots for SRR12813206/SRR12813206.sra Read 9911832 spots for SRR12813207/SRR12813207.sra Written 9911832 spots for SRR12813207/SRR12813207.sra Read 9705959 spots for SRR12813208/SRR12813208.sra Written 9705959 spots for SRR12813208/SRR12813208.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172752 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:20:46 38819802 reads; of these: 38819802 (100.00%) were paired; of these: 30558349 (78.72%) aligned concordantly 0 times 6783000 (17.47%) aligned concordantly exactly 1 time 1478453 (3.81%) aligned concordantly >1 times ---- 30558349 pairs aligned concordantly 0 times; of these: 62611 (0.20%) aligned discordantly 1 time ---- 30495738 pairs aligned 0 times concordantly or discordantly; of these: 60991476 mates make up the pairs; of these: 59546462 (97.63%) aligned 0 times 843505 (1.38%) aligned exactly 1 time 601509 (0.99%) aligned >1 times 23.30% overall alignment rate Time searching: 00:20:47 Overall time: 00:20:47 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] 475127 / 8282999 = 0.0574 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 15:11:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281729/SRX9281729.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281729/SRX9281729.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281729/SRX9281729.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281729/SRX9281729.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 15:11:09: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:11:09: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:11:15: 1000000 INFO @ Sat, 11 Dec 2021 15:11:21: 2000000 INFO @ Sat, 11 Dec 2021 15:11:27: 3000000 INFO @ Sat, 11 Dec 2021 15:11:33: 4000000 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 15:11:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281729/SRX9281729.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281729/SRX9281729.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281729/SRX9281729.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281729/SRX9281729.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 15:11:39: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:11:39: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:11:40: 5000000 INFO @ Sat, 11 Dec 2021 15:11:46: 6000000 INFO @ Sat, 11 Dec 2021 15:11:46: 1000000 INFO @ Sat, 11 Dec 2021 15:11:52: 7000000 INFO @ Sat, 11 Dec 2021 15:11:53: 2000000 INFO @ Sat, 11 Dec 2021 15:11:59: 8000000 INFO @ Sat, 11 Dec 2021 15:11:59: 3000000 INFO @ Sat, 11 Dec 2021 15:12:05: 9000000 INFO @ Sat, 11 Dec 2021 15:12:05: 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 15:12:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281729/SRX9281729.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281729/SRX9281729.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281729/SRX9281729.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281729/SRX9281729.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 15:12:09: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:12:09: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:12:12: 10000000 INFO @ Sat, 11 Dec 2021 15:12:12: 5000000 INFO @ Sat, 11 Dec 2021 15:12:16: 1000000 INFO @ Sat, 11 Dec 2021 15:12:19: 11000000 INFO @ Sat, 11 Dec 2021 15:12:19: 6000000 INFO @ Sat, 11 Dec 2021 15:12:23: 2000000 INFO @ Sat, 11 Dec 2021 15:12:25: 12000000 INFO @ Sat, 11 Dec 2021 15:12:26: 7000000 INFO @ Sat, 11 Dec 2021 15:12:30: 3000000 INFO @ Sat, 11 Dec 2021 15:12:32: 13000000 INFO @ Sat, 11 Dec 2021 15:12:32: 8000000 INFO @ Sat, 11 Dec 2021 15:12:37: 4000000 INFO @ Sat, 11 Dec 2021 15:12:39: 14000000 INFO @ Sat, 11 Dec 2021 15:12:39: 9000000 INFO @ Sat, 11 Dec 2021 15:12:44: 5000000 INFO @ Sat, 11 Dec 2021 15:12:45: 15000000 INFO @ Sat, 11 Dec 2021 15:12:46: 10000000 INFO @ Sat, 11 Dec 2021 15:12:51: 6000000 INFO @ Sat, 11 Dec 2021 15:12:52: 16000000 INFO @ Sat, 11 Dec 2021 15:12:53: 11000000 INFO @ Sat, 11 Dec 2021 15:12:58: 7000000 INFO @ Sat, 11 Dec 2021 15:12:58: 17000000 INFO @ Sat, 11 Dec 2021 15:12:59: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:12:59: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:12:59: #1 total tags in treatment: 7786837 INFO @ Sat, 11 Dec 2021 15:12:59: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:12:59: #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 15:12:59: #1 tags after filtering in treatment: 6949784 INFO @ Sat, 11 Dec 2021 15:12:59: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 11 Dec 2021 15:12:59: #1 finished! INFO @ Sat, 11 Dec 2021 15:12:59: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:12:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:12:59: 12000000 INFO @ Sat, 11 Dec 2021 15:13:00: #2 number of paired peaks: 966 WARNING @ Sat, 11 Dec 2021 15:13:00: Fewer paired peaks (966) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 966 pairs to build model! INFO @ Sat, 11 Dec 2021 15:13:00: start model_add_line... INFO @ Sat, 11 Dec 2021 15:13:00: start X-correlation... INFO @ Sat, 11 Dec 2021 15:13:00: end of X-cor INFO @ Sat, 11 Dec 2021 15:13:00: #2 finished! INFO @ Sat, 11 Dec 2021 15:13:00: #2 predicted fragment length is 141 bps INFO @ Sat, 11 Dec 2021 15:13:00: #2 alternative fragment length(s) may be 3,141 bps INFO @ Sat, 11 Dec 2021 15:13:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281729/SRX9281729.05_model.r INFO @ Sat, 11 Dec 2021 15:13:00: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:13:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:13:04: 8000000 INFO @ Sat, 11 Dec 2021 15:13:06: 13000000 INFO @ Sat, 11 Dec 2021 15:13:11: 9000000 INFO @ Sat, 11 Dec 2021 15:13:13: 14000000 INFO @ Sat, 11 Dec 2021 15:13:16: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:13:18: 10000000 INFO @ Sat, 11 Dec 2021 15:13:19: 15000000 INFO @ Sat, 11 Dec 2021 15:13:24: 11000000 INFO @ Sat, 11 Dec 2021 15:13:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281729/SRX9281729.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:13:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281729/SRX9281729.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:13:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281729/SRX9281729.05_summits.bed INFO @ Sat, 11 Dec 2021 15:13:25: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1107 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:13:25: 16000000 INFO @ Sat, 11 Dec 2021 15:13:31: 12000000 INFO @ Sat, 11 Dec 2021 15:13:32: 17000000 INFO @ Sat, 11 Dec 2021 15:13:33: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:13:33: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:13:33: #1 total tags in treatment: 7786837 INFO @ Sat, 11 Dec 2021 15:13:33: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:13:33: #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 15:13:33: #1 tags after filtering in treatment: 6949784 INFO @ Sat, 11 Dec 2021 15:13:33: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 11 Dec 2021 15:13:33: #1 finished! INFO @ Sat, 11 Dec 2021 15:13:33: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:13:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:13:33: #2 number of paired peaks: 966 WARNING @ Sat, 11 Dec 2021 15:13:33: Fewer paired peaks (966) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 966 pairs to build model! INFO @ Sat, 11 Dec 2021 15:13:33: start model_add_line... INFO @ Sat, 11 Dec 2021 15:13:34: start X-correlation... INFO @ Sat, 11 Dec 2021 15:13:34: end of X-cor INFO @ Sat, 11 Dec 2021 15:13:34: #2 finished! INFO @ Sat, 11 Dec 2021 15:13:34: #2 predicted fragment length is 141 bps INFO @ Sat, 11 Dec 2021 15:13:34: #2 alternative fragment length(s) may be 3,141 bps INFO @ Sat, 11 Dec 2021 15:13:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281729/SRX9281729.10_model.r INFO @ Sat, 11 Dec 2021 15:13:34: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:13:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:13:37: 13000000 INFO @ Sat, 11 Dec 2021 15:13:43: 14000000 INFO @ Sat, 11 Dec 2021 15:13:49: 15000000 INFO @ Sat, 11 Dec 2021 15:13:49: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:13:54: 16000000 INFO @ Sat, 11 Dec 2021 15:13:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281729/SRX9281729.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:13:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281729/SRX9281729.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:13:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281729/SRX9281729.10_summits.bed INFO @ Sat, 11 Dec 2021 15:13:59: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (631 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:14:00: 17000000 INFO @ Sat, 11 Dec 2021 15:14:01: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:14:01: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:14:01: #1 total tags in treatment: 7786837 INFO @ Sat, 11 Dec 2021 15:14:01: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:14:01: #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 15:14:01: #1 tags after filtering in treatment: 6949784 INFO @ Sat, 11 Dec 2021 15:14:01: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 11 Dec 2021 15:14:01: #1 finished! INFO @ Sat, 11 Dec 2021 15:14:01: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:14:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:14:02: #2 number of paired peaks: 966 WARNING @ Sat, 11 Dec 2021 15:14:02: Fewer paired peaks (966) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 966 pairs to build model! INFO @ Sat, 11 Dec 2021 15:14:02: start model_add_line... INFO @ Sat, 11 Dec 2021 15:14:02: start X-correlation... INFO @ Sat, 11 Dec 2021 15:14:02: end of X-cor INFO @ Sat, 11 Dec 2021 15:14:02: #2 finished! INFO @ Sat, 11 Dec 2021 15:14:02: #2 predicted fragment length is 141 bps INFO @ Sat, 11 Dec 2021 15:14:02: #2 alternative fragment length(s) may be 3,141 bps INFO @ Sat, 11 Dec 2021 15:14:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281729/SRX9281729.20_model.r INFO @ Sat, 11 Dec 2021 15:14:02: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:14:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:14:17: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:14:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281729/SRX9281729.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:14:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281729/SRX9281729.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:14:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281729/SRX9281729.20_summits.bed INFO @ Sat, 11 Dec 2021 15:14:26: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (276 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。