Job ID = 14170550 SRX = SRX9720886 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 12477189 spots for SRR13291876/SRR13291876.sra Written 12477189 spots for SRR13291876/SRR13291876.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170953 ("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: 00:03:55 12477189 reads; of these: 12477189 (100.00%) were unpaired; of these: 1039001 (8.33%) aligned 0 times 7777747 (62.34%) aligned exactly 1 time 3660441 (29.34%) aligned >1 times 91.67% overall alignment rate Time searching: 00:03:55 Overall time: 00:03:55 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] 1148566 / 11438188 = 0.1004 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 07:18:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720886/SRX9720886.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720886/SRX9720886.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720886/SRX9720886.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720886/SRX9720886.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 07:18:11: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:18:11: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:18:16: 1000000 INFO @ Sat, 11 Dec 2021 07:18:20: 2000000 INFO @ Sat, 11 Dec 2021 07:18:25: 3000000 INFO @ Sat, 11 Dec 2021 07:18:30: 4000000 INFO @ Sat, 11 Dec 2021 07:18:34: 5000000 INFO @ Sat, 11 Dec 2021 07:18:39: 6000000 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 07:18:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720886/SRX9720886.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720886/SRX9720886.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720886/SRX9720886.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720886/SRX9720886.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 07:18:41: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:18:41: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:18:43: 7000000 INFO @ Sat, 11 Dec 2021 07:18:46: 1000000 INFO @ Sat, 11 Dec 2021 07:18:48: 8000000 INFO @ Sat, 11 Dec 2021 07:18:51: 2000000 INFO @ Sat, 11 Dec 2021 07:18:53: 9000000 INFO @ Sat, 11 Dec 2021 07:18:55: 3000000 INFO @ Sat, 11 Dec 2021 07:18:58: 10000000 INFO @ Sat, 11 Dec 2021 07:18:59: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:18:59: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:18:59: #1 total tags in treatment: 10289622 INFO @ Sat, 11 Dec 2021 07:18:59: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:18:59: #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 07:18:59: #1 tags after filtering in treatment: 10289622 INFO @ Sat, 11 Dec 2021 07:18:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:18:59: #1 finished! INFO @ Sat, 11 Dec 2021 07:18:59: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:18:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:19:00: #2 number of paired peaks: 943 WARNING @ Sat, 11 Dec 2021 07:19:00: Fewer paired peaks (943) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 943 pairs to build model! INFO @ Sat, 11 Dec 2021 07:19:00: start model_add_line... INFO @ Sat, 11 Dec 2021 07:19:00: 4000000 INFO @ Sat, 11 Dec 2021 07:19:00: start X-correlation... INFO @ Sat, 11 Dec 2021 07:19:00: end of X-cor INFO @ Sat, 11 Dec 2021 07:19:00: #2 finished! INFO @ Sat, 11 Dec 2021 07:19:00: #2 predicted fragment length is 195 bps INFO @ Sat, 11 Dec 2021 07:19:00: #2 alternative fragment length(s) may be 195 bps INFO @ Sat, 11 Dec 2021 07:19:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720886/SRX9720886.05_model.r INFO @ Sat, 11 Dec 2021 07:19:00: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:19:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:19:05: 5000000 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 07:19:09: 6000000 INFO @ Sat, 11 Dec 2021 07:19:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720886/SRX9720886.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720886/SRX9720886.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720886/SRX9720886.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720886/SRX9720886.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 07:19:11: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:19:11: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:19:14: 7000000 INFO @ Sat, 11 Dec 2021 07:19:16: 1000000 INFO @ Sat, 11 Dec 2021 07:19:19: 8000000 INFO @ Sat, 11 Dec 2021 07:19:20: 2000000 INFO @ Sat, 11 Dec 2021 07:19:21: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:19:23: 9000000 INFO @ Sat, 11 Dec 2021 07:19:25: 3000000 INFO @ Sat, 11 Dec 2021 07:19:28: 10000000 INFO @ Sat, 11 Dec 2021 07:19:29: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:19:29: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:19:29: #1 total tags in treatment: 10289622 INFO @ Sat, 11 Dec 2021 07:19:29: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:19:29: #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 07:19:29: #1 tags after filtering in treatment: 10289622 INFO @ Sat, 11 Dec 2021 07:19:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:19:29: #1 finished! INFO @ Sat, 11 Dec 2021 07:19:29: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:19:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:19:30: 4000000 INFO @ Sat, 11 Dec 2021 07:19:30: #2 number of paired peaks: 943 WARNING @ Sat, 11 Dec 2021 07:19:30: Fewer paired peaks (943) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 943 pairs to build model! INFO @ Sat, 11 Dec 2021 07:19:30: start model_add_line... INFO @ Sat, 11 Dec 2021 07:19:30: start X-correlation... INFO @ Sat, 11 Dec 2021 07:19:30: end of X-cor INFO @ Sat, 11 Dec 2021 07:19:30: #2 finished! INFO @ Sat, 11 Dec 2021 07:19:30: #2 predicted fragment length is 195 bps INFO @ Sat, 11 Dec 2021 07:19:30: #2 alternative fragment length(s) may be 195 bps INFO @ Sat, 11 Dec 2021 07:19:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720886/SRX9720886.10_model.r INFO @ Sat, 11 Dec 2021 07:19:30: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:19:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:19:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720886/SRX9720886.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:19:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720886/SRX9720886.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:19:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720886/SRX9720886.05_summits.bed INFO @ Sat, 11 Dec 2021 07:19:32: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5100 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:19:34: 5000000 INFO @ Sat, 11 Dec 2021 07:19:39: 6000000 INFO @ Sat, 11 Dec 2021 07:19:44: 7000000 INFO @ Sat, 11 Dec 2021 07:19:48: 8000000 INFO @ Sat, 11 Dec 2021 07:19:52: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:19:53: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:19:57: 10000000 INFO @ Sat, 11 Dec 2021 07:19:59: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:19:59: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:19:59: #1 total tags in treatment: 10289622 INFO @ Sat, 11 Dec 2021 07:19:59: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:19:59: #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 07:19:59: #1 tags after filtering in treatment: 10289622 INFO @ Sat, 11 Dec 2021 07:19:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:19:59: #1 finished! INFO @ Sat, 11 Dec 2021 07:19:59: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:19:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:20:00: #2 number of paired peaks: 943 WARNING @ Sat, 11 Dec 2021 07:20:00: Fewer paired peaks (943) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 943 pairs to build model! INFO @ Sat, 11 Dec 2021 07:20:00: start model_add_line... INFO @ Sat, 11 Dec 2021 07:20:00: start X-correlation... INFO @ Sat, 11 Dec 2021 07:20:00: end of X-cor INFO @ Sat, 11 Dec 2021 07:20:00: #2 finished! INFO @ Sat, 11 Dec 2021 07:20:00: #2 predicted fragment length is 195 bps INFO @ Sat, 11 Dec 2021 07:20:00: #2 alternative fragment length(s) may be 195 bps INFO @ Sat, 11 Dec 2021 07:20:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720886/SRX9720886.20_model.r INFO @ Sat, 11 Dec 2021 07:20:00: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:20:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:20:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720886/SRX9720886.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:20:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720886/SRX9720886.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:20:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720886/SRX9720886.10_summits.bed INFO @ Sat, 11 Dec 2021 07:20:03: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3579 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:20:21: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:20:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720886/SRX9720886.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:20:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720886/SRX9720886.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:20:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720886/SRX9720886.20_summits.bed INFO @ Sat, 11 Dec 2021 07:20:32: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2162 records, 4 fields): 4 millis CompletedMACS2peakCalling