Job ID = 14170621 SRX = SRX8497065 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 23025126 spots for SRR11952664/SRR11952664.sra Written 23025126 spots for SRR11952664/SRR11952664.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171260 ("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: 01:10:45 23025126 reads; of these: 23025126 (100.00%) were paired; of these: 2088247 (9.07%) aligned concordantly 0 times 12327354 (53.54%) aligned concordantly exactly 1 time 8609525 (37.39%) aligned concordantly >1 times ---- 2088247 pairs aligned concordantly 0 times; of these: 370171 (17.73%) aligned discordantly 1 time ---- 1718076 pairs aligned 0 times concordantly or discordantly; of these: 3436152 mates make up the pairs; of these: 2175779 (63.32%) aligned 0 times 549728 (16.00%) aligned exactly 1 time 710645 (20.68%) aligned >1 times 95.28% overall alignment rate Time searching: 01:10:45 Overall time: 01:10:45 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 2144169 / 21256635 = 0.1009 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 08:58:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497065/SRX8497065.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497065/SRX8497065.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497065/SRX8497065.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497065/SRX8497065.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 08:58:28: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:58:28: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:58:33: 1000000 INFO @ Sat, 11 Dec 2021 08:58:38: 2000000 INFO @ Sat, 11 Dec 2021 08:58:44: 3000000 INFO @ Sat, 11 Dec 2021 08:58:49: 4000000 INFO @ Sat, 11 Dec 2021 08:58:54: 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 08:58:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497065/SRX8497065.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497065/SRX8497065.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497065/SRX8497065.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497065/SRX8497065.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 08:58:57: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:58:57: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:59:00: 6000000 INFO @ Sat, 11 Dec 2021 08:59:03: 1000000 INFO @ Sat, 11 Dec 2021 08:59:05: 7000000 INFO @ Sat, 11 Dec 2021 08:59:09: 2000000 INFO @ Sat, 11 Dec 2021 08:59:11: 8000000 INFO @ Sat, 11 Dec 2021 08:59:14: 3000000 INFO @ Sat, 11 Dec 2021 08:59:17: 9000000 INFO @ Sat, 11 Dec 2021 08:59:20: 4000000 INFO @ Sat, 11 Dec 2021 08:59:22: 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 @ Sat, 11 Dec 2021 08:59:26: 5000000 INFO @ Sat, 11 Dec 2021 08:59:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497065/SRX8497065.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497065/SRX8497065.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497065/SRX8497065.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497065/SRX8497065.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 08:59:27: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:59:27: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:59:28: 11000000 INFO @ Sat, 11 Dec 2021 08:59:32: 6000000 INFO @ Sat, 11 Dec 2021 08:59:34: 12000000 INFO @ Sat, 11 Dec 2021 08:59:34: 1000000 INFO @ Sat, 11 Dec 2021 08:59:38: 7000000 INFO @ Sat, 11 Dec 2021 08:59:40: 13000000 INFO @ Sat, 11 Dec 2021 08:59:41: 2000000 INFO @ Sat, 11 Dec 2021 08:59:44: 8000000 INFO @ Sat, 11 Dec 2021 08:59:46: 14000000 INFO @ Sat, 11 Dec 2021 08:59:48: 3000000 INFO @ Sat, 11 Dec 2021 08:59:50: 9000000 INFO @ Sat, 11 Dec 2021 08:59:52: 15000000 INFO @ Sat, 11 Dec 2021 08:59:55: 4000000 INFO @ Sat, 11 Dec 2021 08:59:56: 10000000 INFO @ Sat, 11 Dec 2021 08:59:58: 16000000 INFO @ Sat, 11 Dec 2021 09:00:02: 11000000 INFO @ Sat, 11 Dec 2021 09:00:02: 5000000 INFO @ Sat, 11 Dec 2021 09:00:04: 17000000 INFO @ Sat, 11 Dec 2021 09:00:08: 12000000 INFO @ Sat, 11 Dec 2021 09:00:09: 6000000 INFO @ Sat, 11 Dec 2021 09:00:11: 18000000 INFO @ Sat, 11 Dec 2021 09:00:14: 13000000 INFO @ Sat, 11 Dec 2021 09:00:16: 7000000 INFO @ Sat, 11 Dec 2021 09:00:16: 19000000 INFO @ Sat, 11 Dec 2021 09:00:20: 14000000 INFO @ Sat, 11 Dec 2021 09:00:22: 20000000 INFO @ Sat, 11 Dec 2021 09:00:23: 8000000 INFO @ Sat, 11 Dec 2021 09:00:26: 15000000 INFO @ Sat, 11 Dec 2021 09:00:28: 21000000 INFO @ Sat, 11 Dec 2021 09:00:30: 9000000 INFO @ Sat, 11 Dec 2021 09:00:32: 16000000 INFO @ Sat, 11 Dec 2021 09:00:34: 22000000 INFO @ Sat, 11 Dec 2021 09:00:37: 10000000 INFO @ Sat, 11 Dec 2021 09:00:38: 17000000 INFO @ Sat, 11 Dec 2021 09:00:40: 23000000 INFO @ Sat, 11 Dec 2021 09:00:44: 11000000 INFO @ Sat, 11 Dec 2021 09:00:44: 18000000 INFO @ Sat, 11 Dec 2021 09:00:46: 24000000 INFO @ Sat, 11 Dec 2021 09:00:50: 19000000 INFO @ Sat, 11 Dec 2021 09:00:51: 12000000 INFO @ Sat, 11 Dec 2021 09:00:52: 25000000 INFO @ Sat, 11 Dec 2021 09:00:56: 20000000 INFO @ Sat, 11 Dec 2021 09:00:58: 13000000 INFO @ Sat, 11 Dec 2021 09:00:58: 26000000 INFO @ Sat, 11 Dec 2021 09:01:02: 21000000 INFO @ Sat, 11 Dec 2021 09:01:04: 27000000 INFO @ Sat, 11 Dec 2021 09:01:04: 14000000 INFO @ Sat, 11 Dec 2021 09:01:08: 22000000 INFO @ Sat, 11 Dec 2021 09:01:10: 28000000 INFO @ Sat, 11 Dec 2021 09:01:12: 15000000 INFO @ Sat, 11 Dec 2021 09:01:14: 23000000 INFO @ Sat, 11 Dec 2021 09:01:16: 29000000 INFO @ Sat, 11 Dec 2021 09:01:19: 16000000 INFO @ Sat, 11 Dec 2021 09:01:20: 24000000 INFO @ Sat, 11 Dec 2021 09:01:22: 30000000 INFO @ Sat, 11 Dec 2021 09:01:26: 17000000 INFO @ Sat, 11 Dec 2021 09:01:26: 25000000 INFO @ Sat, 11 Dec 2021 09:01:28: 31000000 INFO @ Sat, 11 Dec 2021 09:01:32: 26000000 INFO @ Sat, 11 Dec 2021 09:01:33: 18000000 INFO @ Sat, 11 Dec 2021 09:01:34: 32000000 INFO @ Sat, 11 Dec 2021 09:01:38: 27000000 INFO @ Sat, 11 Dec 2021 09:01:40: 33000000 INFO @ Sat, 11 Dec 2021 09:01:40: 19000000 INFO @ Sat, 11 Dec 2021 09:01:44: 28000000 INFO @ Sat, 11 Dec 2021 09:01:46: 34000000 INFO @ Sat, 11 Dec 2021 09:01:48: 20000000 INFO @ Sat, 11 Dec 2021 09:01:50: 29000000 INFO @ Sat, 11 Dec 2021 09:01:52: 35000000 INFO @ Sat, 11 Dec 2021 09:01:55: 21000000 INFO @ Sat, 11 Dec 2021 09:01:56: 30000000 INFO @ Sat, 11 Dec 2021 09:01:58: 36000000 INFO @ Sat, 11 Dec 2021 09:02:02: 31000000 INFO @ Sat, 11 Dec 2021 09:02:03: 22000000 INFO @ Sat, 11 Dec 2021 09:02:03: 37000000 INFO @ Sat, 11 Dec 2021 09:02:08: 32000000 INFO @ Sat, 11 Dec 2021 09:02:09: 38000000 INFO @ Sat, 11 Dec 2021 09:02:11: 23000000 INFO @ Sat, 11 Dec 2021 09:02:14: 33000000 INFO @ Sat, 11 Dec 2021 09:02:15: 39000000 INFO @ Sat, 11 Dec 2021 09:02:18: 24000000 INFO @ Sat, 11 Dec 2021 09:02:19: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 09:02:19: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 09:02:19: #1 total tags in treatment: 18816466 INFO @ Sat, 11 Dec 2021 09:02:19: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:02:19: #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 09:02:19: #1 tags after filtering in treatment: 17040209 INFO @ Sat, 11 Dec 2021 09:02:19: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 11 Dec 2021 09:02:19: #1 finished! INFO @ Sat, 11 Dec 2021 09:02:19: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:02:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:02:20: 34000000 INFO @ Sat, 11 Dec 2021 09:02:20: #2 number of paired peaks: 344 WARNING @ Sat, 11 Dec 2021 09:02:20: Fewer paired peaks (344) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 344 pairs to build model! INFO @ Sat, 11 Dec 2021 09:02:20: start model_add_line... INFO @ Sat, 11 Dec 2021 09:02:20: start X-correlation... INFO @ Sat, 11 Dec 2021 09:02:20: end of X-cor INFO @ Sat, 11 Dec 2021 09:02:20: #2 finished! INFO @ Sat, 11 Dec 2021 09:02:20: #2 predicted fragment length is 208 bps INFO @ Sat, 11 Dec 2021 09:02:20: #2 alternative fragment length(s) may be 208 bps INFO @ Sat, 11 Dec 2021 09:02:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497065/SRX8497065.05_model.r INFO @ Sat, 11 Dec 2021 09:02:20: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:02:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:02:26: 35000000 INFO @ Sat, 11 Dec 2021 09:02:26: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:02:32: 36000000 INFO @ Sat, 11 Dec 2021 09:02:34: 26000000 INFO @ Sat, 11 Dec 2021 09:02:38: 37000000 INFO @ Sat, 11 Dec 2021 09:02:42: 27000000 INFO @ Sat, 11 Dec 2021 09:02:43: 38000000 INFO @ Sat, 11 Dec 2021 09:02:49: 39000000 INFO @ Sat, 11 Dec 2021 09:02:49: 28000000 INFO @ Sat, 11 Dec 2021 09:02:53: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:02:53: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 09:02:53: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 09:02:53: #1 total tags in treatment: 18816466 INFO @ Sat, 11 Dec 2021 09:02:53: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:02:53: #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 09:02:53: #1 tags after filtering in treatment: 17040209 INFO @ Sat, 11 Dec 2021 09:02:53: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 11 Dec 2021 09:02:53: #1 finished! INFO @ Sat, 11 Dec 2021 09:02:53: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:02:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:02:54: #2 number of paired peaks: 344 WARNING @ Sat, 11 Dec 2021 09:02:54: Fewer paired peaks (344) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 344 pairs to build model! INFO @ Sat, 11 Dec 2021 09:02:54: start model_add_line... INFO @ Sat, 11 Dec 2021 09:02:54: start X-correlation... INFO @ Sat, 11 Dec 2021 09:02:54: end of X-cor INFO @ Sat, 11 Dec 2021 09:02:54: #2 finished! INFO @ Sat, 11 Dec 2021 09:02:54: #2 predicted fragment length is 208 bps INFO @ Sat, 11 Dec 2021 09:02:54: #2 alternative fragment length(s) may be 208 bps INFO @ Sat, 11 Dec 2021 09:02:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497065/SRX8497065.10_model.r INFO @ Sat, 11 Dec 2021 09:02:54: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:02:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:02:56: 29000000 INFO @ Sat, 11 Dec 2021 09:03:03: 30000000 INFO @ Sat, 11 Dec 2021 09:03:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497065/SRX8497065.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:03:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497065/SRX8497065.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:03:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497065/SRX8497065.05_summits.bed INFO @ Sat, 11 Dec 2021 09:03:09: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (8278 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:03:10: 31000000 INFO @ Sat, 11 Dec 2021 09:03:17: 32000000 INFO @ Sat, 11 Dec 2021 09:03:24: 33000000 INFO @ Sat, 11 Dec 2021 09:03:26: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:03:31: 34000000 INFO @ Sat, 11 Dec 2021 09:03:37: 35000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:03:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497065/SRX8497065.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:03:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497065/SRX8497065.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:03:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497065/SRX8497065.10_summits.bed INFO @ Sat, 11 Dec 2021 09:03:43: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4769 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:03:44: 36000000 INFO @ Sat, 11 Dec 2021 09:03:51: 37000000 INFO @ Sat, 11 Dec 2021 09:03:58: 38000000 INFO @ Sat, 11 Dec 2021 09:04:04: 39000000 INFO @ Sat, 11 Dec 2021 09:04:08: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 09:04:08: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 09:04:08: #1 total tags in treatment: 18816466 INFO @ Sat, 11 Dec 2021 09:04:08: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:04:08: #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 09:04:09: #1 tags after filtering in treatment: 17040209 INFO @ Sat, 11 Dec 2021 09:04:09: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 11 Dec 2021 09:04:09: #1 finished! INFO @ Sat, 11 Dec 2021 09:04:09: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:04:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:04:10: #2 number of paired peaks: 344 WARNING @ Sat, 11 Dec 2021 09:04:10: Fewer paired peaks (344) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 344 pairs to build model! INFO @ Sat, 11 Dec 2021 09:04:10: start model_add_line... INFO @ Sat, 11 Dec 2021 09:04:10: start X-correlation... INFO @ Sat, 11 Dec 2021 09:04:10: end of X-cor INFO @ Sat, 11 Dec 2021 09:04:10: #2 finished! INFO @ Sat, 11 Dec 2021 09:04:10: #2 predicted fragment length is 208 bps INFO @ Sat, 11 Dec 2021 09:04:10: #2 alternative fragment length(s) may be 208 bps INFO @ Sat, 11 Dec 2021 09:04:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497065/SRX8497065.20_model.r INFO @ Sat, 11 Dec 2021 09:04:10: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:04:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:04:43: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:04:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497065/SRX8497065.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:04:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497065/SRX8497065.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:04:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497065/SRX8497065.20_summits.bed INFO @ Sat, 11 Dec 2021 09:04:59: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2162 records, 4 fields): 4 millis CompletedMACS2peakCalling