Job ID = 14167110 SRX = SRX4712932 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 44306640 spots for SRR7874062/SRR7874062.sra Written 44306640 spots for SRR7874062/SRR7874062.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167563 ("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: 00:15:27 44306640 reads; of these: 44306640 (100.00%) were unpaired; of these: 1306392 (2.95%) aligned 0 times 35771550 (80.74%) aligned exactly 1 time 7228698 (16.32%) aligned >1 times 97.05% overall alignment rate Time searching: 00:15:27 Overall time: 00:15:27 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 20 files... [bam_rmdupse_core] 14295599 / 43000248 = 0.3325 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 @ Fri, 10 Dec 2021 10:25:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4712932/SRX4712932.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4712932/SRX4712932.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4712932/SRX4712932.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4712932/SRX4712932.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 @ Fri, 10 Dec 2021 10:25:36: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:25:36: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:25:42: 1000000 INFO @ Fri, 10 Dec 2021 10:25:47: 2000000 INFO @ Fri, 10 Dec 2021 10:25:52: 3000000 INFO @ Fri, 10 Dec 2021 10:25:57: 4000000 INFO @ Fri, 10 Dec 2021 10:26:02: 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 @ Fri, 10 Dec 2021 10:26:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4712932/SRX4712932.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4712932/SRX4712932.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4712932/SRX4712932.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4712932/SRX4712932.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 @ Fri, 10 Dec 2021 10:26:06: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:26:06: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:26:08: 6000000 INFO @ Fri, 10 Dec 2021 10:26:12: 1000000 INFO @ Fri, 10 Dec 2021 10:26:13: 7000000 INFO @ Fri, 10 Dec 2021 10:26:18: 2000000 INFO @ Fri, 10 Dec 2021 10:26:19: 8000000 INFO @ Fri, 10 Dec 2021 10:26:24: 3000000 INFO @ Fri, 10 Dec 2021 10:26:25: 9000000 INFO @ Fri, 10 Dec 2021 10:26:30: 4000000 INFO @ Fri, 10 Dec 2021 10:26:30: 10000000 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 @ Fri, 10 Dec 2021 10:26:35: 5000000 INFO @ Fri, 10 Dec 2021 10:26:36: 11000000 INFO @ Fri, 10 Dec 2021 10:26:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4712932/SRX4712932.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4712932/SRX4712932.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4712932/SRX4712932.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4712932/SRX4712932.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 @ Fri, 10 Dec 2021 10:26:37: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:26:37: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:26:41: 6000000 INFO @ Fri, 10 Dec 2021 10:26:42: 12000000 INFO @ Fri, 10 Dec 2021 10:26:42: 1000000 INFO @ Fri, 10 Dec 2021 10:26:47: 7000000 INFO @ Fri, 10 Dec 2021 10:26:48: 13000000 INFO @ Fri, 10 Dec 2021 10:26:48: 2000000 INFO @ Fri, 10 Dec 2021 10:26:53: 8000000 INFO @ Fri, 10 Dec 2021 10:26:53: 14000000 INFO @ Fri, 10 Dec 2021 10:26:54: 3000000 INFO @ Fri, 10 Dec 2021 10:26:59: 9000000 INFO @ Fri, 10 Dec 2021 10:26:59: 15000000 INFO @ Fri, 10 Dec 2021 10:27:00: 4000000 INFO @ Fri, 10 Dec 2021 10:27:04: 10000000 INFO @ Fri, 10 Dec 2021 10:27:05: 16000000 INFO @ Fri, 10 Dec 2021 10:27:06: 5000000 INFO @ Fri, 10 Dec 2021 10:27:10: 11000000 INFO @ Fri, 10 Dec 2021 10:27:11: 17000000 INFO @ Fri, 10 Dec 2021 10:27:12: 6000000 INFO @ Fri, 10 Dec 2021 10:27:16: 12000000 INFO @ Fri, 10 Dec 2021 10:27:16: 18000000 INFO @ Fri, 10 Dec 2021 10:27:18: 7000000 INFO @ Fri, 10 Dec 2021 10:27:22: 13000000 INFO @ Fri, 10 Dec 2021 10:27:22: 19000000 INFO @ Fri, 10 Dec 2021 10:27:23: 8000000 INFO @ Fri, 10 Dec 2021 10:27:28: 14000000 INFO @ Fri, 10 Dec 2021 10:27:28: 20000000 INFO @ Fri, 10 Dec 2021 10:27:29: 9000000 INFO @ Fri, 10 Dec 2021 10:27:33: 15000000 INFO @ Fri, 10 Dec 2021 10:27:34: 21000000 INFO @ Fri, 10 Dec 2021 10:27:35: 10000000 INFO @ Fri, 10 Dec 2021 10:27:39: 16000000 INFO @ Fri, 10 Dec 2021 10:27:39: 22000000 INFO @ Fri, 10 Dec 2021 10:27:41: 11000000 INFO @ Fri, 10 Dec 2021 10:27:45: 17000000 INFO @ Fri, 10 Dec 2021 10:27:45: 23000000 INFO @ Fri, 10 Dec 2021 10:27:47: 12000000 INFO @ Fri, 10 Dec 2021 10:27:51: 18000000 INFO @ Fri, 10 Dec 2021 10:27:51: 24000000 INFO @ Fri, 10 Dec 2021 10:27:52: 13000000 INFO @ Fri, 10 Dec 2021 10:27:57: 19000000 INFO @ Fri, 10 Dec 2021 10:27:57: 25000000 INFO @ Fri, 10 Dec 2021 10:27:58: 14000000 INFO @ Fri, 10 Dec 2021 10:28:02: 20000000 INFO @ Fri, 10 Dec 2021 10:28:03: 26000000 INFO @ Fri, 10 Dec 2021 10:28:04: 15000000 INFO @ Fri, 10 Dec 2021 10:28:08: 21000000 INFO @ Fri, 10 Dec 2021 10:28:08: 27000000 INFO @ Fri, 10 Dec 2021 10:28:10: 16000000 INFO @ Fri, 10 Dec 2021 10:28:14: 22000000 INFO @ Fri, 10 Dec 2021 10:28:14: 28000000 INFO @ Fri, 10 Dec 2021 10:28:16: 17000000 INFO @ Fri, 10 Dec 2021 10:28:19: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 10:28:19: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 10:28:19: #1 total tags in treatment: 28704649 INFO @ Fri, 10 Dec 2021 10:28:19: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:28:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 10:28:19: #1 tags after filtering in treatment: 28704649 INFO @ Fri, 10 Dec 2021 10:28:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:28:19: #1 finished! INFO @ Fri, 10 Dec 2021 10:28:19: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:28:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:28:20: 23000000 INFO @ Fri, 10 Dec 2021 10:28:21: #2 number of paired peaks: 426 WARNING @ Fri, 10 Dec 2021 10:28:21: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Fri, 10 Dec 2021 10:28:21: start model_add_line... INFO @ Fri, 10 Dec 2021 10:28:21: start X-correlation... INFO @ Fri, 10 Dec 2021 10:28:21: end of X-cor INFO @ Fri, 10 Dec 2021 10:28:21: #2 finished! INFO @ Fri, 10 Dec 2021 10:28:21: #2 predicted fragment length is 121 bps INFO @ Fri, 10 Dec 2021 10:28:21: #2 alternative fragment length(s) may be 121 bps INFO @ Fri, 10 Dec 2021 10:28:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4712932/SRX4712932.05_model.r INFO @ Fri, 10 Dec 2021 10:28:21: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:28:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:28:21: 18000000 INFO @ Fri, 10 Dec 2021 10:28:26: 24000000 INFO @ Fri, 10 Dec 2021 10:28:27: 19000000 INFO @ Fri, 10 Dec 2021 10:28:32: 25000000 INFO @ Fri, 10 Dec 2021 10:28:33: 20000000 INFO @ Fri, 10 Dec 2021 10:28:37: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 10:28:39: 21000000 INFO @ Fri, 10 Dec 2021 10:28:43: 27000000 INFO @ Fri, 10 Dec 2021 10:28:44: 22000000 INFO @ Fri, 10 Dec 2021 10:28:49: 28000000 INFO @ Fri, 10 Dec 2021 10:28:50: 23000000 INFO @ Fri, 10 Dec 2021 10:28:53: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 10:28:53: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 10:28:53: #1 total tags in treatment: 28704649 INFO @ Fri, 10 Dec 2021 10:28:53: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:28:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 10:28:54: #1 tags after filtering in treatment: 28704649 INFO @ Fri, 10 Dec 2021 10:28:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:28:54: #1 finished! INFO @ Fri, 10 Dec 2021 10:28:54: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:28:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:28:56: #2 number of paired peaks: 426 WARNING @ Fri, 10 Dec 2021 10:28:56: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Fri, 10 Dec 2021 10:28:56: start model_add_line... INFO @ Fri, 10 Dec 2021 10:28:56: 24000000 INFO @ Fri, 10 Dec 2021 10:28:56: start X-correlation... INFO @ Fri, 10 Dec 2021 10:28:56: end of X-cor INFO @ Fri, 10 Dec 2021 10:28:56: #2 finished! INFO @ Fri, 10 Dec 2021 10:28:56: #2 predicted fragment length is 121 bps INFO @ Fri, 10 Dec 2021 10:28:56: #2 alternative fragment length(s) may be 121 bps INFO @ Fri, 10 Dec 2021 10:28:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4712932/SRX4712932.10_model.r INFO @ Fri, 10 Dec 2021 10:28:56: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:28:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:29:01: 25000000 INFO @ Fri, 10 Dec 2021 10:29:07: 26000000 INFO @ Fri, 10 Dec 2021 10:29:12: 27000000 INFO @ Fri, 10 Dec 2021 10:29:15: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:29:18: 28000000 INFO @ Fri, 10 Dec 2021 10:29:22: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 10:29:22: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 10:29:22: #1 total tags in treatment: 28704649 INFO @ Fri, 10 Dec 2021 10:29:22: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:29:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 10:29:22: #1 tags after filtering in treatment: 28704649 INFO @ Fri, 10 Dec 2021 10:29:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:29:22: #1 finished! INFO @ Fri, 10 Dec 2021 10:29:22: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:29:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:29:24: #2 number of paired peaks: 426 WARNING @ Fri, 10 Dec 2021 10:29:24: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Fri, 10 Dec 2021 10:29:24: start model_add_line... INFO @ Fri, 10 Dec 2021 10:29:24: start X-correlation... INFO @ Fri, 10 Dec 2021 10:29:24: end of X-cor INFO @ Fri, 10 Dec 2021 10:29:24: #2 finished! INFO @ Fri, 10 Dec 2021 10:29:24: #2 predicted fragment length is 121 bps INFO @ Fri, 10 Dec 2021 10:29:24: #2 alternative fragment length(s) may be 121 bps INFO @ Fri, 10 Dec 2021 10:29:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4712932/SRX4712932.20_model.r INFO @ Fri, 10 Dec 2021 10:29:24: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:29:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 10:29:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4712932/SRX4712932.05_peaks.xls INFO @ Fri, 10 Dec 2021 10:29:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4712932/SRX4712932.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:29:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4712932/SRX4712932.05_summits.bed INFO @ Fri, 10 Dec 2021 10:29:42: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11495 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:29:51: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:30:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4712932/SRX4712932.10_peaks.xls INFO @ Fri, 10 Dec 2021 10:30:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4712932/SRX4712932.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:30:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4712932/SRX4712932.10_summits.bed INFO @ Fri, 10 Dec 2021 10:30:18: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (8400 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:30:19: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:30:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4712932/SRX4712932.20_peaks.xls INFO @ Fri, 10 Dec 2021 10:30:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4712932/SRX4712932.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:30:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4712932/SRX4712932.20_summits.bed INFO @ Fri, 10 Dec 2021 10:30:45: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5963 records, 4 fields): 7 millis CompletedMACS2peakCalling