Job ID = 16438091 SRX = SRX10031704 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 34370847 spots for SRR13634474/SRR13634474.sra Written 34370847 spots for SRR13634474/SRR13634474.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438431 ("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: 00:12:44 34370847 reads; of these: 34370847 (100.00%) were unpaired; of these: 1116660 (3.25%) aligned 0 times 27522737 (80.08%) aligned exactly 1 time 5731450 (16.68%) aligned >1 times 96.75% overall alignment rate Time searching: 00:12:44 Overall time: 00:12:44 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 16 files... [bam_rmdupse_core] 8007823 / 33254187 = 0.2408 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 13:56:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031704/SRX10031704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031704/SRX10031704.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031704/SRX10031704.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10031704/SRX10031704.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 13:56:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:56:37: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:56:43: 1000000 INFO @ Tue, 02 Aug 2022 13:56:49: 2000000 INFO @ Tue, 02 Aug 2022 13:56:56: 3000000 INFO @ Tue, 02 Aug 2022 13:57:02: 4000000 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 13:57:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031704/SRX10031704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031704/SRX10031704.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031704/SRX10031704.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10031704/SRX10031704.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 13:57:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:57:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:57:08: 5000000 INFO @ Tue, 02 Aug 2022 13:57:13: 1000000 INFO @ Tue, 02 Aug 2022 13:57:15: 6000000 INFO @ Tue, 02 Aug 2022 13:57:19: 2000000 INFO @ Tue, 02 Aug 2022 13:57:21: 7000000 INFO @ Tue, 02 Aug 2022 13:57:25: 3000000 INFO @ Tue, 02 Aug 2022 13:57:27: 8000000 INFO @ Tue, 02 Aug 2022 13:57:32: 4000000 INFO @ Tue, 02 Aug 2022 13:57:34: 9000000 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 13:57:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031704/SRX10031704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031704/SRX10031704.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031704/SRX10031704.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10031704/SRX10031704.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 13:57:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:57:37: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:57:38: 5000000 INFO @ Tue, 02 Aug 2022 13:57:40: 10000000 INFO @ Tue, 02 Aug 2022 13:57:43: 1000000 INFO @ Tue, 02 Aug 2022 13:57:44: 6000000 INFO @ Tue, 02 Aug 2022 13:57:46: 11000000 INFO @ Tue, 02 Aug 2022 13:57:49: 2000000 INFO @ Tue, 02 Aug 2022 13:57:50: 7000000 INFO @ Tue, 02 Aug 2022 13:57:52: 12000000 INFO @ Tue, 02 Aug 2022 13:57:56: 3000000 INFO @ Tue, 02 Aug 2022 13:57:56: 8000000 INFO @ Tue, 02 Aug 2022 13:57:58: 13000000 INFO @ Tue, 02 Aug 2022 13:58:02: 9000000 INFO @ Tue, 02 Aug 2022 13:58:02: 4000000 INFO @ Tue, 02 Aug 2022 13:58:04: 14000000 INFO @ Tue, 02 Aug 2022 13:58:08: 10000000 INFO @ Tue, 02 Aug 2022 13:58:08: 5000000 INFO @ Tue, 02 Aug 2022 13:58:10: 15000000 INFO @ Tue, 02 Aug 2022 13:58:14: 11000000 INFO @ Tue, 02 Aug 2022 13:58:14: 6000000 INFO @ Tue, 02 Aug 2022 13:58:16: 16000000 INFO @ Tue, 02 Aug 2022 13:58:19: 12000000 INFO @ Tue, 02 Aug 2022 13:58:21: 7000000 INFO @ Tue, 02 Aug 2022 13:58:22: 17000000 INFO @ Tue, 02 Aug 2022 13:58:25: 13000000 INFO @ Tue, 02 Aug 2022 13:58:27: 8000000 INFO @ Tue, 02 Aug 2022 13:58:28: 18000000 INFO @ Tue, 02 Aug 2022 13:58:31: 14000000 INFO @ Tue, 02 Aug 2022 13:58:33: 9000000 INFO @ Tue, 02 Aug 2022 13:58:35: 19000000 INFO @ Tue, 02 Aug 2022 13:58:37: 15000000 INFO @ Tue, 02 Aug 2022 13:58:39: 10000000 INFO @ Tue, 02 Aug 2022 13:58:41: 20000000 INFO @ Tue, 02 Aug 2022 13:58:43: 16000000 INFO @ Tue, 02 Aug 2022 13:58:45: 11000000 INFO @ Tue, 02 Aug 2022 13:58:48: 21000000 INFO @ Tue, 02 Aug 2022 13:58:49: 17000000 INFO @ Tue, 02 Aug 2022 13:58:50: 12000000 INFO @ Tue, 02 Aug 2022 13:58:54: 22000000 INFO @ Tue, 02 Aug 2022 13:58:55: 18000000 INFO @ Tue, 02 Aug 2022 13:58:56: 13000000 INFO @ Tue, 02 Aug 2022 13:59:00: 23000000 INFO @ Tue, 02 Aug 2022 13:59:01: 19000000 INFO @ Tue, 02 Aug 2022 13:59:02: 14000000 INFO @ Tue, 02 Aug 2022 13:59:06: 24000000 INFO @ Tue, 02 Aug 2022 13:59:08: 20000000 INFO @ Tue, 02 Aug 2022 13:59:08: 15000000 INFO @ Tue, 02 Aug 2022 13:59:13: 25000000 INFO @ Tue, 02 Aug 2022 13:59:14: 16000000 INFO @ Tue, 02 Aug 2022 13:59:14: 21000000 INFO @ Tue, 02 Aug 2022 13:59:14: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 13:59:14: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 13:59:14: #1 total tags in treatment: 25246364 INFO @ Tue, 02 Aug 2022 13:59:14: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:59:14: #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 13:59:15: #1 tags after filtering in treatment: 25246364 INFO @ Tue, 02 Aug 2022 13:59:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:59:15: #1 finished! INFO @ Tue, 02 Aug 2022 13:59:15: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:59:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:59:16: #2 number of paired peaks: 182 WARNING @ Tue, 02 Aug 2022 13:59:16: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Tue, 02 Aug 2022 13:59:16: start model_add_line... INFO @ Tue, 02 Aug 2022 13:59:16: start X-correlation... INFO @ Tue, 02 Aug 2022 13:59:17: end of X-cor INFO @ Tue, 02 Aug 2022 13:59:17: #2 finished! INFO @ Tue, 02 Aug 2022 13:59:17: #2 predicted fragment length is 168 bps INFO @ Tue, 02 Aug 2022 13:59:17: #2 alternative fragment length(s) may be 4,168 bps INFO @ Tue, 02 Aug 2022 13:59:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031704/SRX10031704.05_model.r INFO @ Tue, 02 Aug 2022 13:59:17: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:59:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:59:20: 17000000 INFO @ Tue, 02 Aug 2022 13:59:20: 22000000 INFO @ Tue, 02 Aug 2022 13:59:25: 23000000 INFO @ Tue, 02 Aug 2022 13:59:25: 18000000 INFO @ Tue, 02 Aug 2022 13:59:31: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:59:31: 19000000 INFO @ Tue, 02 Aug 2022 13:59:37: 25000000 INFO @ Tue, 02 Aug 2022 13:59:38: 20000000 INFO @ Tue, 02 Aug 2022 13:59:39: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 13:59:39: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 13:59:39: #1 total tags in treatment: 25246364 INFO @ Tue, 02 Aug 2022 13:59:39: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:59:39: #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 13:59:39: #1 tags after filtering in treatment: 25246364 INFO @ Tue, 02 Aug 2022 13:59:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:59:39: #1 finished! INFO @ Tue, 02 Aug 2022 13:59:39: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:59:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:59:41: #2 number of paired peaks: 182 WARNING @ Tue, 02 Aug 2022 13:59:41: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Tue, 02 Aug 2022 13:59:41: start model_add_line... INFO @ Tue, 02 Aug 2022 13:59:41: start X-correlation... INFO @ Tue, 02 Aug 2022 13:59:41: end of X-cor INFO @ Tue, 02 Aug 2022 13:59:41: #2 finished! INFO @ Tue, 02 Aug 2022 13:59:41: #2 predicted fragment length is 168 bps INFO @ Tue, 02 Aug 2022 13:59:41: #2 alternative fragment length(s) may be 4,168 bps INFO @ Tue, 02 Aug 2022 13:59:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031704/SRX10031704.10_model.r INFO @ Tue, 02 Aug 2022 13:59:41: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:59:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:59:44: 21000000 INFO @ Tue, 02 Aug 2022 13:59:49: 22000000 INFO @ Tue, 02 Aug 2022 13:59:55: 23000000 INFO @ Tue, 02 Aug 2022 14:00:01: 24000000 INFO @ Tue, 02 Aug 2022 14:00:05: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:00:07: 25000000 INFO @ Tue, 02 Aug 2022 14:00:08: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:00:08: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:00:08: #1 total tags in treatment: 25246364 INFO @ Tue, 02 Aug 2022 14:00:08: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:00:08: #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 14:00:09: #1 tags after filtering in treatment: 25246364 INFO @ Tue, 02 Aug 2022 14:00:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:00:09: #1 finished! INFO @ Tue, 02 Aug 2022 14:00:09: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:00:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:00:10: #2 number of paired peaks: 182 WARNING @ Tue, 02 Aug 2022 14:00:10: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Tue, 02 Aug 2022 14:00:10: start model_add_line... INFO @ Tue, 02 Aug 2022 14:00:10: start X-correlation... INFO @ Tue, 02 Aug 2022 14:00:10: end of X-cor INFO @ Tue, 02 Aug 2022 14:00:10: #2 finished! INFO @ Tue, 02 Aug 2022 14:00:10: #2 predicted fragment length is 168 bps INFO @ Tue, 02 Aug 2022 14:00:10: #2 alternative fragment length(s) may be 4,168 bps INFO @ Tue, 02 Aug 2022 14:00:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031704/SRX10031704.20_model.r INFO @ Tue, 02 Aug 2022 14:00:10: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:00:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:00:29: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:00:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031704/SRX10031704.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:00:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031704/SRX10031704.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:00:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031704/SRX10031704.05_summits.bed INFO @ Tue, 02 Aug 2022 14:00:30: Done! BigWig に変換しました。 pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5707 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:00:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031704/SRX10031704.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:00:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031704/SRX10031704.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:00:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031704/SRX10031704.10_summits.bed INFO @ Tue, 02 Aug 2022 14:00:53: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3401 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:01:00: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:01:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031704/SRX10031704.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:01:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031704/SRX10031704.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:01:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031704/SRX10031704.20_summits.bed INFO @ Tue, 02 Aug 2022 14:01:24: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1496 records, 4 fields): 22 millis CompletedMACS2peakCalling