Job ID = 14171249 SRX = SRX9986125 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 21282879 spots for SRR13591544/SRR13591544.sra Written 21282879 spots for SRR13591544/SRR13591544.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171713 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:40 21282879 reads; of these: 21282879 (100.00%) were unpaired; of these: 1959783 (9.21%) aligned 0 times 16531181 (77.67%) aligned exactly 1 time 2791915 (13.12%) aligned >1 times 90.79% overall alignment rate Time searching: 00:05:41 Overall time: 00:05:41 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_rmdupse_core] 6972793 / 19323096 = 0.3609 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 10:54:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986125/SRX9986125.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986125/SRX9986125.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986125/SRX9986125.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986125/SRX9986125.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 10:54:37: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:54:37: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:54:47: 1000000 INFO @ Sat, 11 Dec 2021 10:54:58: 2000000 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 10:55:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986125/SRX9986125.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986125/SRX9986125.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986125/SRX9986125.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986125/SRX9986125.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 10:55:07: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:55:07: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:55:08: 3000000 INFO @ Sat, 11 Dec 2021 10:55:18: 1000000 INFO @ Sat, 11 Dec 2021 10:55:18: 4000000 INFO @ Sat, 11 Dec 2021 10:55:28: 5000000 INFO @ Sat, 11 Dec 2021 10:55:29: 2000000 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 10:55:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986125/SRX9986125.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986125/SRX9986125.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986125/SRX9986125.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986125/SRX9986125.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 10:55:37: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:55:37: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:55:38: 6000000 INFO @ Sat, 11 Dec 2021 10:55:40: 3000000 INFO @ Sat, 11 Dec 2021 10:55:48: 7000000 INFO @ Sat, 11 Dec 2021 10:55:49: 1000000 INFO @ Sat, 11 Dec 2021 10:55:51: 4000000 INFO @ Sat, 11 Dec 2021 10:55:58: 8000000 INFO @ Sat, 11 Dec 2021 10:55:59: 2000000 INFO @ Sat, 11 Dec 2021 10:56:02: 5000000 INFO @ Sat, 11 Dec 2021 10:56:09: 9000000 INFO @ Sat, 11 Dec 2021 10:56:09: 3000000 INFO @ Sat, 11 Dec 2021 10:56:13: 6000000 INFO @ Sat, 11 Dec 2021 10:56:19: 10000000 INFO @ Sat, 11 Dec 2021 10:56:19: 4000000 INFO @ Sat, 11 Dec 2021 10:56:24: 7000000 INFO @ Sat, 11 Dec 2021 10:56:29: 11000000 INFO @ Sat, 11 Dec 2021 10:56:30: 5000000 INFO @ Sat, 11 Dec 2021 10:56:36: 8000000 INFO @ Sat, 11 Dec 2021 10:56:39: 12000000 INFO @ Sat, 11 Dec 2021 10:56:40: 6000000 INFO @ Sat, 11 Dec 2021 10:56:43: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 10:56:43: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 10:56:43: #1 total tags in treatment: 12350303 INFO @ Sat, 11 Dec 2021 10:56:43: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:56:43: #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 10:56:43: #1 tags after filtering in treatment: 12350303 INFO @ Sat, 11 Dec 2021 10:56:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 10:56:43: #1 finished! INFO @ Sat, 11 Dec 2021 10:56:43: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:56:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:56:44: #2 number of paired peaks: 566 WARNING @ Sat, 11 Dec 2021 10:56:44: Fewer paired peaks (566) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 566 pairs to build model! INFO @ Sat, 11 Dec 2021 10:56:44: start model_add_line... INFO @ Sat, 11 Dec 2021 10:56:44: start X-correlation... INFO @ Sat, 11 Dec 2021 10:56:44: end of X-cor INFO @ Sat, 11 Dec 2021 10:56:44: #2 finished! INFO @ Sat, 11 Dec 2021 10:56:44: #2 predicted fragment length is 255 bps INFO @ Sat, 11 Dec 2021 10:56:44: #2 alternative fragment length(s) may be 255 bps INFO @ Sat, 11 Dec 2021 10:56:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986125/SRX9986125.05_model.r INFO @ Sat, 11 Dec 2021 10:56:44: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:56:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:56:47: 9000000 INFO @ Sat, 11 Dec 2021 10:56:51: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 10:56:58: 10000000 INFO @ Sat, 11 Dec 2021 10:57:01: 8000000 INFO @ Sat, 11 Dec 2021 10:57:09: 11000000 INFO @ Sat, 11 Dec 2021 10:57:11: 9000000 INFO @ Sat, 11 Dec 2021 10:57:17: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:57:20: 12000000 INFO @ Sat, 11 Dec 2021 10:57:22: 10000000 INFO @ Sat, 11 Dec 2021 10:57:24: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 10:57:24: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 10:57:24: #1 total tags in treatment: 12350303 INFO @ Sat, 11 Dec 2021 10:57:24: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:57:24: #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 10:57:24: #1 tags after filtering in treatment: 12350303 INFO @ Sat, 11 Dec 2021 10:57:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 10:57:24: #1 finished! INFO @ Sat, 11 Dec 2021 10:57:24: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:57:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:57:25: #2 number of paired peaks: 566 WARNING @ Sat, 11 Dec 2021 10:57:25: Fewer paired peaks (566) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 566 pairs to build model! INFO @ Sat, 11 Dec 2021 10:57:25: start model_add_line... INFO @ Sat, 11 Dec 2021 10:57:25: start X-correlation... INFO @ Sat, 11 Dec 2021 10:57:25: end of X-cor INFO @ Sat, 11 Dec 2021 10:57:25: #2 finished! INFO @ Sat, 11 Dec 2021 10:57:25: #2 predicted fragment length is 255 bps INFO @ Sat, 11 Dec 2021 10:57:25: #2 alternative fragment length(s) may be 255 bps INFO @ Sat, 11 Dec 2021 10:57:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986125/SRX9986125.10_model.r INFO @ Sat, 11 Dec 2021 10:57:25: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:57:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 10:57:32: 11000000 INFO @ Sat, 11 Dec 2021 10:57:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986125/SRX9986125.05_peaks.xls INFO @ Sat, 11 Dec 2021 10:57:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986125/SRX9986125.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:57:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986125/SRX9986125.05_summits.bed INFO @ Sat, 11 Dec 2021 10:57:34: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (6413 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 10:57:43: 12000000 INFO @ Sat, 11 Dec 2021 10:57:46: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 10:57:46: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 10:57:46: #1 total tags in treatment: 12350303 INFO @ Sat, 11 Dec 2021 10:57:46: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:57:46: #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 10:57:46: #1 tags after filtering in treatment: 12350303 INFO @ Sat, 11 Dec 2021 10:57:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 10:57:46: #1 finished! INFO @ Sat, 11 Dec 2021 10:57:46: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:57:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:57:47: #2 number of paired peaks: 566 WARNING @ Sat, 11 Dec 2021 10:57:47: Fewer paired peaks (566) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 566 pairs to build model! INFO @ Sat, 11 Dec 2021 10:57:47: start model_add_line... INFO @ Sat, 11 Dec 2021 10:57:47: start X-correlation... INFO @ Sat, 11 Dec 2021 10:57:47: end of X-cor INFO @ Sat, 11 Dec 2021 10:57:47: #2 finished! INFO @ Sat, 11 Dec 2021 10:57:47: #2 predicted fragment length is 255 bps INFO @ Sat, 11 Dec 2021 10:57:47: #2 alternative fragment length(s) may be 255 bps INFO @ Sat, 11 Dec 2021 10:57:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986125/SRX9986125.20_model.r INFO @ Sat, 11 Dec 2021 10:57:47: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:57:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:57:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:58:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986125/SRX9986125.10_peaks.xls INFO @ Sat, 11 Dec 2021 10:58:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986125/SRX9986125.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:58:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986125/SRX9986125.10_summits.bed INFO @ Sat, 11 Dec 2021 10:58:17: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (2687 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 10:58:19: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:58:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986125/SRX9986125.20_peaks.xls INFO @ Sat, 11 Dec 2021 10:58:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986125/SRX9986125.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:58:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986125/SRX9986125.20_summits.bed INFO @ Sat, 11 Dec 2021 10:58:36: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (725 records, 4 fields): 10 millis CompletedMACS2peakCalling