Job ID = 14170551 SRX = SRX9720887 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 13878543 spots for SRR13291877/SRR13291877.sra Written 13878543 spots for SRR13291877/SRR13291877.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170958 ("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: 00:05:10 13878543 reads; of these: 13878543 (100.00%) were unpaired; of these: 864995 (6.23%) aligned 0 times 8824960 (63.59%) aligned exactly 1 time 4188588 (30.18%) aligned >1 times 93.77% overall alignment rate Time searching: 00:05:10 Overall time: 00:05:10 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] 1232430 / 13013548 = 0.0947 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 07:21:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720887/SRX9720887.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720887/SRX9720887.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720887/SRX9720887.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720887/SRX9720887.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 07:21:06: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:21:06: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:21:12: 1000000 INFO @ Sat, 11 Dec 2021 07:21:17: 2000000 INFO @ Sat, 11 Dec 2021 07:21:23: 3000000 INFO @ Sat, 11 Dec 2021 07:21:28: 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 07:21:34: 5000000 INFO @ Sat, 11 Dec 2021 07:21:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720887/SRX9720887.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720887/SRX9720887.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720887/SRX9720887.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720887/SRX9720887.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 07:21:36: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:21:36: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:21:40: 6000000 INFO @ Sat, 11 Dec 2021 07:21:42: 1000000 INFO @ Sat, 11 Dec 2021 07:21:46: 7000000 INFO @ Sat, 11 Dec 2021 07:21:49: 2000000 INFO @ Sat, 11 Dec 2021 07:21:52: 8000000 INFO @ Sat, 11 Dec 2021 07:21:55: 3000000 INFO @ Sat, 11 Dec 2021 07:21:58: 9000000 INFO @ Sat, 11 Dec 2021 07:22:02: 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 07:22:04: 10000000 INFO @ Sat, 11 Dec 2021 07:22:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720887/SRX9720887.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720887/SRX9720887.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720887/SRX9720887.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720887/SRX9720887.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 07:22:06: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:22:06: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:22:08: 5000000 INFO @ Sat, 11 Dec 2021 07:22:11: 11000000 INFO @ Sat, 11 Dec 2021 07:22:13: 1000000 INFO @ Sat, 11 Dec 2021 07:22:15: 6000000 INFO @ Sat, 11 Dec 2021 07:22:16: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:22:16: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:22:16: #1 total tags in treatment: 11781118 INFO @ Sat, 11 Dec 2021 07:22:16: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:22:16: #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 07:22:16: #1 tags after filtering in treatment: 11781118 INFO @ Sat, 11 Dec 2021 07:22:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:22:16: #1 finished! INFO @ Sat, 11 Dec 2021 07:22:16: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:22:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:22:17: #2 number of paired peaks: 587 WARNING @ Sat, 11 Dec 2021 07:22:17: Fewer paired peaks (587) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 587 pairs to build model! INFO @ Sat, 11 Dec 2021 07:22:17: start model_add_line... INFO @ Sat, 11 Dec 2021 07:22:17: start X-correlation... INFO @ Sat, 11 Dec 2021 07:22:17: end of X-cor INFO @ Sat, 11 Dec 2021 07:22:17: #2 finished! INFO @ Sat, 11 Dec 2021 07:22:17: #2 predicted fragment length is 165 bps INFO @ Sat, 11 Dec 2021 07:22:17: #2 alternative fragment length(s) may be 165 bps INFO @ Sat, 11 Dec 2021 07:22:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720887/SRX9720887.05_model.r INFO @ Sat, 11 Dec 2021 07:22:17: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:22:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:22:20: 2000000 INFO @ Sat, 11 Dec 2021 07:22:21: 7000000 INFO @ Sat, 11 Dec 2021 07:22:26: 3000000 INFO @ Sat, 11 Dec 2021 07:22:27: 8000000 INFO @ Sat, 11 Dec 2021 07:22:33: 9000000 INFO @ Sat, 11 Dec 2021 07:22:33: 4000000 INFO @ Sat, 11 Dec 2021 07:22:39: 10000000 INFO @ Sat, 11 Dec 2021 07:22:40: 5000000 INFO @ Sat, 11 Dec 2021 07:22:41: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:22:45: 11000000 INFO @ Sat, 11 Dec 2021 07:22:46: 6000000 INFO @ Sat, 11 Dec 2021 07:22:49: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:22:51: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:22:51: #1 total tags in treatment: 11781118 INFO @ Sat, 11 Dec 2021 07:22:51: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:22:51: #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 07:22:51: #1 tags after filtering in treatment: 11781118 INFO @ Sat, 11 Dec 2021 07:22:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:22:51: #1 finished! INFO @ Sat, 11 Dec 2021 07:22:51: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:22:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:22:52: #2 number of paired peaks: 587 WARNING @ Sat, 11 Dec 2021 07:22:52: Fewer paired peaks (587) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 587 pairs to build model! INFO @ Sat, 11 Dec 2021 07:22:52: start model_add_line... INFO @ Sat, 11 Dec 2021 07:22:52: start X-correlation... INFO @ Sat, 11 Dec 2021 07:22:52: end of X-cor INFO @ Sat, 11 Dec 2021 07:22:52: #2 finished! INFO @ Sat, 11 Dec 2021 07:22:52: #2 predicted fragment length is 165 bps INFO @ Sat, 11 Dec 2021 07:22:52: #2 alternative fragment length(s) may be 165 bps INFO @ Sat, 11 Dec 2021 07:22:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720887/SRX9720887.10_model.r INFO @ Sat, 11 Dec 2021 07:22:52: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:22:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:22:53: 7000000 INFO @ Sat, 11 Dec 2021 07:22:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720887/SRX9720887.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:22:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720887/SRX9720887.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:22:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720887/SRX9720887.05_summits.bed INFO @ Sat, 11 Dec 2021 07:22:55: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4411 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:22:59: 8000000 INFO @ Sat, 11 Dec 2021 07:23:06: 9000000 INFO @ Sat, 11 Dec 2021 07:23:13: 10000000 INFO @ Sat, 11 Dec 2021 07:23:16: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:23:19: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:23:24: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:23:24: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:23:24: #1 total tags in treatment: 11781118 INFO @ Sat, 11 Dec 2021 07:23:24: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:23:24: #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 07:23:24: #1 tags after filtering in treatment: 11781118 INFO @ Sat, 11 Dec 2021 07:23:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:23:24: #1 finished! INFO @ Sat, 11 Dec 2021 07:23:24: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:23:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:23:25: #2 number of paired peaks: 587 WARNING @ Sat, 11 Dec 2021 07:23:25: Fewer paired peaks (587) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 587 pairs to build model! INFO @ Sat, 11 Dec 2021 07:23:25: start model_add_line... INFO @ Sat, 11 Dec 2021 07:23:25: start X-correlation... INFO @ Sat, 11 Dec 2021 07:23:25: end of X-cor INFO @ Sat, 11 Dec 2021 07:23:25: #2 finished! INFO @ Sat, 11 Dec 2021 07:23:25: #2 predicted fragment length is 165 bps INFO @ Sat, 11 Dec 2021 07:23:25: #2 alternative fragment length(s) may be 165 bps INFO @ Sat, 11 Dec 2021 07:23:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720887/SRX9720887.20_model.r INFO @ Sat, 11 Dec 2021 07:23:25: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:23:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:23:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720887/SRX9720887.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:23:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720887/SRX9720887.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:23:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720887/SRX9720887.10_summits.bed INFO @ Sat, 11 Dec 2021 07:23:30: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2989 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:23:50: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:24:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720887/SRX9720887.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:24:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720887/SRX9720887.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:24:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720887/SRX9720887.20_summits.bed INFO @ Sat, 11 Dec 2021 07:24:06: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1682 records, 4 fields): 7 millis CompletedMACS2peakCalling