Job ID = 16439709 SRX = SRX14237853 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 32138058 spots for SRR18086351/SRR18086351.sra Written 32138058 spots for SRR18086351/SRR18086351.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439840 ("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: 00:13:26 32138058 reads; of these: 32138058 (100.00%) were unpaired; of these: 1643273 (5.11%) aligned 0 times 24878425 (77.41%) aligned exactly 1 time 5616360 (17.48%) aligned >1 times 94.89% overall alignment rate Time searching: 00:13:26 Overall time: 00:13:26 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] 5168449 / 30494785 = 0.1695 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 16:25:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14237853/SRX14237853.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14237853/SRX14237853.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14237853/SRX14237853.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14237853/SRX14237853.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 16:25:31: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:25:31: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:25:39: 1000000 INFO @ Tue, 02 Aug 2022 16:25:47: 2000000 INFO @ Tue, 02 Aug 2022 16:25:54: 3000000 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 16:25:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14237853/SRX14237853.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14237853/SRX14237853.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14237853/SRX14237853.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14237853/SRX14237853.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 16:25:59: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:25:59: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:26:02: 4000000 INFO @ Tue, 02 Aug 2022 16:26:07: 1000000 INFO @ Tue, 02 Aug 2022 16:26:10: 5000000 INFO @ Tue, 02 Aug 2022 16:26:15: 2000000 INFO @ Tue, 02 Aug 2022 16:26:18: 6000000 INFO @ Tue, 02 Aug 2022 16:26:23: 3000000 INFO @ Tue, 02 Aug 2022 16:26:26: 7000000 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 16:26:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14237853/SRX14237853.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14237853/SRX14237853.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14237853/SRX14237853.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14237853/SRX14237853.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 16:26:29: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:26:29: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:26:30: 4000000 INFO @ Tue, 02 Aug 2022 16:26:34: 8000000 INFO @ Tue, 02 Aug 2022 16:26:38: 1000000 INFO @ Tue, 02 Aug 2022 16:26:38: 5000000 INFO @ Tue, 02 Aug 2022 16:26:42: 9000000 INFO @ Tue, 02 Aug 2022 16:26:46: 2000000 INFO @ Tue, 02 Aug 2022 16:26:46: 6000000 INFO @ Tue, 02 Aug 2022 16:26:50: 10000000 INFO @ Tue, 02 Aug 2022 16:26:54: 3000000 INFO @ Tue, 02 Aug 2022 16:26:55: 7000000 INFO @ Tue, 02 Aug 2022 16:26:58: 11000000 INFO @ Tue, 02 Aug 2022 16:27:02: 4000000 INFO @ Tue, 02 Aug 2022 16:27:03: 8000000 INFO @ Tue, 02 Aug 2022 16:27:06: 12000000 INFO @ Tue, 02 Aug 2022 16:27:10: 5000000 INFO @ Tue, 02 Aug 2022 16:27:11: 9000000 INFO @ Tue, 02 Aug 2022 16:27:14: 13000000 INFO @ Tue, 02 Aug 2022 16:27:18: 6000000 INFO @ Tue, 02 Aug 2022 16:27:19: 10000000 INFO @ Tue, 02 Aug 2022 16:27:22: 14000000 INFO @ Tue, 02 Aug 2022 16:27:27: 7000000 INFO @ Tue, 02 Aug 2022 16:27:27: 11000000 INFO @ Tue, 02 Aug 2022 16:27:30: 15000000 INFO @ Tue, 02 Aug 2022 16:27:35: 8000000 INFO @ Tue, 02 Aug 2022 16:27:35: 12000000 INFO @ Tue, 02 Aug 2022 16:27:38: 16000000 INFO @ Tue, 02 Aug 2022 16:27:43: 9000000 INFO @ Tue, 02 Aug 2022 16:27:43: 13000000 INFO @ Tue, 02 Aug 2022 16:27:46: 17000000 INFO @ Tue, 02 Aug 2022 16:27:51: 10000000 INFO @ Tue, 02 Aug 2022 16:27:51: 14000000 INFO @ Tue, 02 Aug 2022 16:27:54: 18000000 INFO @ Tue, 02 Aug 2022 16:27:59: 11000000 INFO @ Tue, 02 Aug 2022 16:28:00: 15000000 INFO @ Tue, 02 Aug 2022 16:28:02: 19000000 INFO @ Tue, 02 Aug 2022 16:28:07: 12000000 INFO @ Tue, 02 Aug 2022 16:28:08: 16000000 INFO @ Tue, 02 Aug 2022 16:28:10: 20000000 INFO @ Tue, 02 Aug 2022 16:28:15: 13000000 INFO @ Tue, 02 Aug 2022 16:28:16: 17000000 INFO @ Tue, 02 Aug 2022 16:28:18: 21000000 INFO @ Tue, 02 Aug 2022 16:28:24: 14000000 INFO @ Tue, 02 Aug 2022 16:28:24: 18000000 INFO @ Tue, 02 Aug 2022 16:28:26: 22000000 INFO @ Tue, 02 Aug 2022 16:28:32: 15000000 INFO @ Tue, 02 Aug 2022 16:28:32: 19000000 INFO @ Tue, 02 Aug 2022 16:28:35: 23000000 INFO @ Tue, 02 Aug 2022 16:28:40: 16000000 INFO @ Tue, 02 Aug 2022 16:28:40: 20000000 INFO @ Tue, 02 Aug 2022 16:28:43: 24000000 INFO @ Tue, 02 Aug 2022 16:28:48: 17000000 INFO @ Tue, 02 Aug 2022 16:28:49: 21000000 INFO @ Tue, 02 Aug 2022 16:28:51: 25000000 INFO @ Tue, 02 Aug 2022 16:28:54: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 16:28:54: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 16:28:54: #1 total tags in treatment: 25326336 INFO @ Tue, 02 Aug 2022 16:28:54: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:28:54: #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 16:28:55: #1 tags after filtering in treatment: 25326336 INFO @ Tue, 02 Aug 2022 16:28:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:28:55: #1 finished! INFO @ Tue, 02 Aug 2022 16:28:55: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:28:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:28:56: 18000000 INFO @ Tue, 02 Aug 2022 16:28:56: #2 number of paired peaks: 996 WARNING @ Tue, 02 Aug 2022 16:28:56: Fewer paired peaks (996) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 996 pairs to build model! INFO @ Tue, 02 Aug 2022 16:28:56: start model_add_line... INFO @ Tue, 02 Aug 2022 16:28:57: start X-correlation... INFO @ Tue, 02 Aug 2022 16:28:57: end of X-cor INFO @ Tue, 02 Aug 2022 16:28:57: #2 finished! INFO @ Tue, 02 Aug 2022 16:28:57: #2 predicted fragment length is 221 bps INFO @ Tue, 02 Aug 2022 16:28:57: #2 alternative fragment length(s) may be 221 bps INFO @ Tue, 02 Aug 2022 16:28:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14237853/SRX14237853.05_model.r INFO @ Tue, 02 Aug 2022 16:28:57: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:28:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:28:58: 22000000 INFO @ Tue, 02 Aug 2022 16:29:04: 19000000 INFO @ Tue, 02 Aug 2022 16:29:06: 23000000 INFO @ Tue, 02 Aug 2022 16:29:12: 20000000 INFO @ Tue, 02 Aug 2022 16:29:14: 24000000 INFO @ Tue, 02 Aug 2022 16:29:21: 21000000 INFO @ Tue, 02 Aug 2022 16:29:22: 25000000 INFO @ Tue, 02 Aug 2022 16:29:25: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 16:29:25: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 16:29:25: #1 total tags in treatment: 25326336 INFO @ Tue, 02 Aug 2022 16:29:25: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:29:25: #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 16:29:26: #1 tags after filtering in treatment: 25326336 INFO @ Tue, 02 Aug 2022 16:29:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:29:26: #1 finished! INFO @ Tue, 02 Aug 2022 16:29:26: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:29:26: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 16:29:27: #2 number of paired peaks: 996 WARNING @ Tue, 02 Aug 2022 16:29:27: Fewer paired peaks (996) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 996 pairs to build model! INFO @ Tue, 02 Aug 2022 16:29:27: start model_add_line... INFO @ Tue, 02 Aug 2022 16:29:28: start X-correlation... INFO @ Tue, 02 Aug 2022 16:29:28: end of X-cor INFO @ Tue, 02 Aug 2022 16:29:28: #2 finished! INFO @ Tue, 02 Aug 2022 16:29:28: #2 predicted fragment length is 221 bps INFO @ Tue, 02 Aug 2022 16:29:28: #2 alternative fragment length(s) may be 221 bps INFO @ Tue, 02 Aug 2022 16:29:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14237853/SRX14237853.10_model.r INFO @ Tue, 02 Aug 2022 16:29:28: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:29:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:29:29: 22000000 INFO @ Tue, 02 Aug 2022 16:29:37: 23000000 INFO @ Tue, 02 Aug 2022 16:29:45: 24000000 INFO @ Tue, 02 Aug 2022 16:29:53: 25000000 INFO @ Tue, 02 Aug 2022 16:29:56: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 16:29:56: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 16:29:56: #1 total tags in treatment: 25326336 INFO @ Tue, 02 Aug 2022 16:29:56: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:29:56: #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 16:29:57: #1 tags after filtering in treatment: 25326336 INFO @ Tue, 02 Aug 2022 16:29:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:29:57: #1 finished! INFO @ Tue, 02 Aug 2022 16:29:57: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:29:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:29:58: #2 number of paired peaks: 996 WARNING @ Tue, 02 Aug 2022 16:29:58: Fewer paired peaks (996) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 996 pairs to build model! INFO @ Tue, 02 Aug 2022 16:29:58: start model_add_line... INFO @ Tue, 02 Aug 2022 16:29:59: start X-correlation... INFO @ Tue, 02 Aug 2022 16:29:59: end of X-cor INFO @ Tue, 02 Aug 2022 16:29:59: #2 finished! INFO @ Tue, 02 Aug 2022 16:29:59: #2 predicted fragment length is 221 bps INFO @ Tue, 02 Aug 2022 16:29:59: #2 alternative fragment length(s) may be 221 bps INFO @ Tue, 02 Aug 2022 16:29:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14237853/SRX14237853.20_model.r INFO @ Tue, 02 Aug 2022 16:29:59: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:29:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:30:00: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:30:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14237853/SRX14237853.05_peaks.xls INFO @ Tue, 02 Aug 2022 16:30:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14237853/SRX14237853.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:30:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14237853/SRX14237853.05_summits.bed INFO @ Tue, 02 Aug 2022 16:30:25: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7263 records, 4 fields): 101 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:30:30: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 16:30:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14237853/SRX14237853.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:30:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14237853/SRX14237853.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:30:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14237853/SRX14237853.10_summits.bed INFO @ Tue, 02 Aug 2022 16:30:56: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5925 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:31:01: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:31:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14237853/SRX14237853.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:31:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14237853/SRX14237853.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:31:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14237853/SRX14237853.20_summits.bed INFO @ Tue, 02 Aug 2022 16:31:26: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4325 records, 4 fields): 53 millis CompletedMACS2peakCalling