Job ID = 14171025 SRX = SRX10000671 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 39306852 spots for SRR13606527/SRR13606527.sra Written 39306852 spots for SRR13606527/SRR13606527.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171495 ("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: 00:07:07 39306852 reads; of these: 39306852 (100.00%) were unpaired; of these: 26094332 (66.39%) aligned 0 times 9645236 (24.54%) aligned exactly 1 time 3567284 (9.08%) aligned >1 times 33.61% overall alignment rate Time searching: 00:07:07 Overall time: 00:07:07 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] 2606774 / 13212520 = 0.1973 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 09:25:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10000671/SRX10000671.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10000671/SRX10000671.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10000671/SRX10000671.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10000671/SRX10000671.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 09:25:17: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:25:17: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:25:23: 1000000 INFO @ Sat, 11 Dec 2021 09:25:28: 2000000 INFO @ Sat, 11 Dec 2021 09:25:34: 3000000 INFO @ Sat, 11 Dec 2021 09:25:39: 4000000 INFO @ Sat, 11 Dec 2021 09:25:44: 5000000 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 09:25:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10000671/SRX10000671.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10000671/SRX10000671.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10000671/SRX10000671.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10000671/SRX10000671.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 09:25:47: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:25:47: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:25:49: 6000000 INFO @ Sat, 11 Dec 2021 09:25:54: 1000000 INFO @ Sat, 11 Dec 2021 09:25:54: 7000000 INFO @ Sat, 11 Dec 2021 09:26:00: 8000000 INFO @ Sat, 11 Dec 2021 09:26:00: 2000000 INFO @ Sat, 11 Dec 2021 09:26:05: 9000000 INFO @ Sat, 11 Dec 2021 09:26:07: 3000000 INFO @ Sat, 11 Dec 2021 09:26:10: 10000000 INFO @ Sat, 11 Dec 2021 09:26:13: 4000000 INFO @ Sat, 11 Dec 2021 09:26:14: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 09:26:14: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 09:26:14: #1 total tags in treatment: 10605746 INFO @ Sat, 11 Dec 2021 09:26:14: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:26:14: #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 09:26:14: #1 tags after filtering in treatment: 10605746 INFO @ Sat, 11 Dec 2021 09:26:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:26:14: #1 finished! INFO @ Sat, 11 Dec 2021 09:26:14: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:26:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:26:15: #2 number of paired peaks: 676 WARNING @ Sat, 11 Dec 2021 09:26:15: Fewer paired peaks (676) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 676 pairs to build model! INFO @ Sat, 11 Dec 2021 09:26:15: start model_add_line... BedGraph に変換中... INFO @ Sat, 11 Dec 2021 09:26:15: start X-correlation... INFO @ Sat, 11 Dec 2021 09:26:15: end of X-cor INFO @ Sat, 11 Dec 2021 09:26:15: #2 finished! INFO @ Sat, 11 Dec 2021 09:26:15: #2 predicted fragment length is 152 bps INFO @ Sat, 11 Dec 2021 09:26:15: #2 alternative fragment length(s) may be 152 bps INFO @ Sat, 11 Dec 2021 09:26:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10000671/SRX10000671.05_model.r INFO @ Sat, 11 Dec 2021 09:26:15: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:26:15: #3 Pre-compute pvalue-qvalue table... 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 09:26:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10000671/SRX10000671.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10000671/SRX10000671.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10000671/SRX10000671.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10000671/SRX10000671.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 09:26:17: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:26:17: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:26:20: 5000000 INFO @ Sat, 11 Dec 2021 09:26:23: 1000000 INFO @ Sat, 11 Dec 2021 09:26:26: 6000000 INFO @ Sat, 11 Dec 2021 09:26:28: 2000000 INFO @ Sat, 11 Dec 2021 09:26:33: 7000000 INFO @ Sat, 11 Dec 2021 09:26:33: 3000000 INFO @ Sat, 11 Dec 2021 09:26:38: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:26:39: 4000000 INFO @ Sat, 11 Dec 2021 09:26:39: 8000000 INFO @ Sat, 11 Dec 2021 09:26:44: 5000000 INFO @ Sat, 11 Dec 2021 09:26:46: 9000000 INFO @ Sat, 11 Dec 2021 09:26:50: 6000000 INFO @ Sat, 11 Dec 2021 09:26:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10000671/SRX10000671.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:26:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10000671/SRX10000671.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:26:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10000671/SRX10000671.05_summits.bed INFO @ Sat, 11 Dec 2021 09:26:52: Done! INFO @ Sat, 11 Dec 2021 09:26:52: 10000000 pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5486 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:26:55: 7000000 INFO @ Sat, 11 Dec 2021 09:26:58: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 09:26:58: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 09:26:58: #1 total tags in treatment: 10605746 INFO @ Sat, 11 Dec 2021 09:26:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:26:58: #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 09:26:58: #1 tags after filtering in treatment: 10605746 INFO @ Sat, 11 Dec 2021 09:26:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:26:58: #1 finished! INFO @ Sat, 11 Dec 2021 09:26:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:26:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:26:59: #2 number of paired peaks: 676 WARNING @ Sat, 11 Dec 2021 09:26:59: Fewer paired peaks (676) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 676 pairs to build model! INFO @ Sat, 11 Dec 2021 09:26:59: start model_add_line... INFO @ Sat, 11 Dec 2021 09:26:59: start X-correlation... INFO @ Sat, 11 Dec 2021 09:26:59: end of X-cor INFO @ Sat, 11 Dec 2021 09:26:59: #2 finished! INFO @ Sat, 11 Dec 2021 09:26:59: #2 predicted fragment length is 152 bps INFO @ Sat, 11 Dec 2021 09:26:59: #2 alternative fragment length(s) may be 152 bps INFO @ Sat, 11 Dec 2021 09:26:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10000671/SRX10000671.10_model.r INFO @ Sat, 11 Dec 2021 09:26:59: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:26:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:27:02: 8000000 INFO @ Sat, 11 Dec 2021 09:27:07: 9000000 INFO @ Sat, 11 Dec 2021 09:27:13: 10000000 INFO @ Sat, 11 Dec 2021 09:27:16: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 09:27:16: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 09:27:16: #1 total tags in treatment: 10605746 INFO @ Sat, 11 Dec 2021 09:27:16: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:27:16: #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 09:27:16: #1 tags after filtering in treatment: 10605746 INFO @ Sat, 11 Dec 2021 09:27:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:27:16: #1 finished! INFO @ Sat, 11 Dec 2021 09:27:16: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:27:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:27:17: #2 number of paired peaks: 676 WARNING @ Sat, 11 Dec 2021 09:27:17: Fewer paired peaks (676) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 676 pairs to build model! INFO @ Sat, 11 Dec 2021 09:27:17: start model_add_line... INFO @ Sat, 11 Dec 2021 09:27:17: start X-correlation... INFO @ Sat, 11 Dec 2021 09:27:17: end of X-cor INFO @ Sat, 11 Dec 2021 09:27:17: #2 finished! INFO @ Sat, 11 Dec 2021 09:27:17: #2 predicted fragment length is 152 bps INFO @ Sat, 11 Dec 2021 09:27:17: #2 alternative fragment length(s) may be 152 bps INFO @ Sat, 11 Dec 2021 09:27:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10000671/SRX10000671.20_model.r INFO @ Sat, 11 Dec 2021 09:27:17: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:27:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:27:23: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:27:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10000671/SRX10000671.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:27:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10000671/SRX10000671.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:27:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10000671/SRX10000671.10_summits.bed INFO @ Sat, 11 Dec 2021 09:27:37: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1873 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:27:41: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:27:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10000671/SRX10000671.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:27:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10000671/SRX10000671.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:27:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10000671/SRX10000671.20_summits.bed INFO @ Sat, 11 Dec 2021 09:27:54: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (559 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。