Job ID = 14171986 SRX = SRX7889141 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21911101 spots for SRR11283131/SRR11283131.sra Written 21911101 spots for SRR11283131/SRR11283131.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172643 ("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: 01:02:39 21911101 reads; of these: 21911101 (100.00%) were paired; of these: 6535526 (29.83%) aligned concordantly 0 times 11350585 (51.80%) aligned concordantly exactly 1 time 4024990 (18.37%) aligned concordantly >1 times ---- 6535526 pairs aligned concordantly 0 times; of these: 1260369 (19.28%) aligned discordantly 1 time ---- 5275157 pairs aligned 0 times concordantly or discordantly; of these: 10550314 mates make up the pairs; of these: 8569022 (81.22%) aligned 0 times 1000622 (9.48%) aligned exactly 1 time 980670 (9.30%) aligned >1 times 80.45% overall alignment rate Time searching: 01:02:39 Overall time: 01:02:39 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 28 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] 1482333 / 15413985 = 0.0962 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 15:01:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7889141/SRX7889141.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7889141/SRX7889141.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7889141/SRX7889141.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7889141/SRX7889141.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 15:01:59: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:01:59: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:02:05: 1000000 INFO @ Sat, 11 Dec 2021 15:02:11: 2000000 INFO @ Sat, 11 Dec 2021 15:02:17: 3000000 INFO @ Sat, 11 Dec 2021 15:02:24: 4000000 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 15:02:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7889141/SRX7889141.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7889141/SRX7889141.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7889141/SRX7889141.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7889141/SRX7889141.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 15:02:28: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:02:28: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:02:30: 5000000 INFO @ Sat, 11 Dec 2021 15:02:36: 1000000 INFO @ Sat, 11 Dec 2021 15:02:36: 6000000 INFO @ Sat, 11 Dec 2021 15:02:43: 7000000 INFO @ Sat, 11 Dec 2021 15:02:44: 2000000 INFO @ Sat, 11 Dec 2021 15:02:49: 8000000 INFO @ Sat, 11 Dec 2021 15:02:52: 3000000 INFO @ Sat, 11 Dec 2021 15:02:56: 9000000 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 15:02:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7889141/SRX7889141.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7889141/SRX7889141.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7889141/SRX7889141.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7889141/SRX7889141.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 15:02:58: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:02:58: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:03:01: 4000000 INFO @ Sat, 11 Dec 2021 15:03:02: 10000000 INFO @ Sat, 11 Dec 2021 15:03:05: 1000000 INFO @ Sat, 11 Dec 2021 15:03:09: 5000000 INFO @ Sat, 11 Dec 2021 15:03:09: 11000000 INFO @ Sat, 11 Dec 2021 15:03:11: 2000000 INFO @ Sat, 11 Dec 2021 15:03:15: 12000000 INFO @ Sat, 11 Dec 2021 15:03:17: 6000000 INFO @ Sat, 11 Dec 2021 15:03:18: 3000000 INFO @ Sat, 11 Dec 2021 15:03:22: 13000000 INFO @ Sat, 11 Dec 2021 15:03:24: 4000000 INFO @ Sat, 11 Dec 2021 15:03:25: 7000000 INFO @ Sat, 11 Dec 2021 15:03:28: 14000000 INFO @ Sat, 11 Dec 2021 15:03:31: 5000000 INFO @ Sat, 11 Dec 2021 15:03:33: 8000000 INFO @ Sat, 11 Dec 2021 15:03:35: 15000000 INFO @ Sat, 11 Dec 2021 15:03:37: 6000000 INFO @ Sat, 11 Dec 2021 15:03:41: 16000000 INFO @ Sat, 11 Dec 2021 15:03:41: 9000000 INFO @ Sat, 11 Dec 2021 15:03:44: 7000000 INFO @ Sat, 11 Dec 2021 15:03:48: 17000000 INFO @ Sat, 11 Dec 2021 15:03:50: 10000000 INFO @ Sat, 11 Dec 2021 15:03:50: 8000000 INFO @ Sat, 11 Dec 2021 15:03:54: 18000000 INFO @ Sat, 11 Dec 2021 15:03:57: 9000000 INFO @ Sat, 11 Dec 2021 15:03:58: 11000000 INFO @ Sat, 11 Dec 2021 15:04:01: 19000000 INFO @ Sat, 11 Dec 2021 15:04:04: 10000000 INFO @ Sat, 11 Dec 2021 15:04:06: 12000000 INFO @ Sat, 11 Dec 2021 15:04:07: 20000000 INFO @ Sat, 11 Dec 2021 15:04:10: 11000000 INFO @ Sat, 11 Dec 2021 15:04:14: 13000000 INFO @ Sat, 11 Dec 2021 15:04:14: 21000000 INFO @ Sat, 11 Dec 2021 15:04:17: 12000000 INFO @ Sat, 11 Dec 2021 15:04:21: 22000000 INFO @ Sat, 11 Dec 2021 15:04:22: 14000000 INFO @ Sat, 11 Dec 2021 15:04:23: 13000000 INFO @ Sat, 11 Dec 2021 15:04:27: 23000000 INFO @ Sat, 11 Dec 2021 15:04:30: 14000000 INFO @ Sat, 11 Dec 2021 15:04:30: 15000000 INFO @ Sat, 11 Dec 2021 15:04:34: 24000000 INFO @ Sat, 11 Dec 2021 15:04:36: 15000000 INFO @ Sat, 11 Dec 2021 15:04:38: 16000000 INFO @ Sat, 11 Dec 2021 15:04:40: 25000000 INFO @ Sat, 11 Dec 2021 15:04:43: 16000000 INFO @ Sat, 11 Dec 2021 15:04:46: 17000000 INFO @ Sat, 11 Dec 2021 15:04:47: 26000000 INFO @ Sat, 11 Dec 2021 15:04:49: 17000000 INFO @ Sat, 11 Dec 2021 15:04:53: 27000000 INFO @ Sat, 11 Dec 2021 15:04:54: 18000000 INFO @ Sat, 11 Dec 2021 15:04:56: 18000000 INFO @ Sat, 11 Dec 2021 15:05:00: 28000000 INFO @ Sat, 11 Dec 2021 15:05:02: 19000000 INFO @ Sat, 11 Dec 2021 15:05:04: 19000000 INFO @ Sat, 11 Dec 2021 15:05:06: 29000000 INFO @ Sat, 11 Dec 2021 15:05:10: 20000000 INFO @ Sat, 11 Dec 2021 15:05:11: 20000000 INFO @ Sat, 11 Dec 2021 15:05:13: 30000000 INFO @ Sat, 11 Dec 2021 15:05:18: 21000000 INFO @ Sat, 11 Dec 2021 15:05:19: 21000000 INFO @ Sat, 11 Dec 2021 15:05:19: 31000000 INFO @ Sat, 11 Dec 2021 15:05:26: 32000000 INFO @ Sat, 11 Dec 2021 15:05:27: 22000000 INFO @ Sat, 11 Dec 2021 15:05:27: 22000000 INFO @ Sat, 11 Dec 2021 15:05:28: #1 tag size is determined as 118 bps INFO @ Sat, 11 Dec 2021 15:05:28: #1 tag size = 118 INFO @ Sat, 11 Dec 2021 15:05:28: #1 total tags in treatment: 13974631 INFO @ Sat, 11 Dec 2021 15:05:28: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:05:28: #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 15:05:28: #1 tags after filtering in treatment: 13245739 INFO @ Sat, 11 Dec 2021 15:05:28: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 11 Dec 2021 15:05:28: #1 finished! INFO @ Sat, 11 Dec 2021 15:05:28: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:05:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:05:29: #2 number of paired peaks: 236 WARNING @ Sat, 11 Dec 2021 15:05:29: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Sat, 11 Dec 2021 15:05:29: start model_add_line... INFO @ Sat, 11 Dec 2021 15:05:29: start X-correlation... INFO @ Sat, 11 Dec 2021 15:05:29: end of X-cor INFO @ Sat, 11 Dec 2021 15:05:29: #2 finished! INFO @ Sat, 11 Dec 2021 15:05:29: #2 predicted fragment length is 248 bps INFO @ Sat, 11 Dec 2021 15:05:29: #2 alternative fragment length(s) may be 248 bps INFO @ Sat, 11 Dec 2021 15:05:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7889141/SRX7889141.05_model.r INFO @ Sat, 11 Dec 2021 15:05:29: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:05:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:05:35: 23000000 INFO @ Sat, 11 Dec 2021 15:05:35: 23000000 INFO @ Sat, 11 Dec 2021 15:05:43: 24000000 INFO @ Sat, 11 Dec 2021 15:05:43: 24000000 INFO @ Sat, 11 Dec 2021 15:05:51: 25000000 INFO @ Sat, 11 Dec 2021 15:05:52: 25000000 INFO @ Sat, 11 Dec 2021 15:05:56: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:05:59: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:06:00: 26000000 INFO @ Sat, 11 Dec 2021 15:06:07: 27000000 INFO @ Sat, 11 Dec 2021 15:06:08: 27000000 INFO @ Sat, 11 Dec 2021 15:06:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7889141/SRX7889141.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:06:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7889141/SRX7889141.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:06:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7889141/SRX7889141.05_summits.bed INFO @ Sat, 11 Dec 2021 15:06:09: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5344 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:06:15: 28000000 INFO @ Sat, 11 Dec 2021 15:06:16: 28000000 INFO @ Sat, 11 Dec 2021 15:06:23: 29000000 INFO @ Sat, 11 Dec 2021 15:06:24: 29000000 INFO @ Sat, 11 Dec 2021 15:06:32: 30000000 INFO @ Sat, 11 Dec 2021 15:06:32: 30000000 INFO @ Sat, 11 Dec 2021 15:06:40: 31000000 INFO @ Sat, 11 Dec 2021 15:06:40: 31000000 INFO @ Sat, 11 Dec 2021 15:06:48: 32000000 INFO @ Sat, 11 Dec 2021 15:06:48: 32000000 INFO @ Sat, 11 Dec 2021 15:06:50: #1 tag size is determined as 118 bps INFO @ Sat, 11 Dec 2021 15:06:50: #1 tag size = 118 INFO @ Sat, 11 Dec 2021 15:06:50: #1 total tags in treatment: 13974631 INFO @ Sat, 11 Dec 2021 15:06:50: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:06:50: #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 15:06:50: #1 tags after filtering in treatment: 13245739 INFO @ Sat, 11 Dec 2021 15:06:50: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 11 Dec 2021 15:06:50: #1 finished! INFO @ Sat, 11 Dec 2021 15:06:50: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:06:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:06:51: #1 tag size is determined as 118 bps INFO @ Sat, 11 Dec 2021 15:06:51: #1 tag size = 118 INFO @ Sat, 11 Dec 2021 15:06:51: #1 total tags in treatment: 13974631 INFO @ Sat, 11 Dec 2021 15:06:51: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:06:51: #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 15:06:51: #1 tags after filtering in treatment: 13245739 INFO @ Sat, 11 Dec 2021 15:06:51: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 11 Dec 2021 15:06:51: #1 finished! INFO @ Sat, 11 Dec 2021 15:06:51: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:06:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:06:51: #2 number of paired peaks: 236 WARNING @ Sat, 11 Dec 2021 15:06:51: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Sat, 11 Dec 2021 15:06:51: start model_add_line... INFO @ Sat, 11 Dec 2021 15:06:51: start X-correlation... INFO @ Sat, 11 Dec 2021 15:06:51: end of X-cor INFO @ Sat, 11 Dec 2021 15:06:51: #2 finished! INFO @ Sat, 11 Dec 2021 15:06:51: #2 predicted fragment length is 248 bps INFO @ Sat, 11 Dec 2021 15:06:51: #2 alternative fragment length(s) may be 248 bps INFO @ Sat, 11 Dec 2021 15:06:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7889141/SRX7889141.10_model.r INFO @ Sat, 11 Dec 2021 15:06:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:06:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:06:52: #2 number of paired peaks: 236 WARNING @ Sat, 11 Dec 2021 15:06:52: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Sat, 11 Dec 2021 15:06:52: start model_add_line... INFO @ Sat, 11 Dec 2021 15:06:52: start X-correlation... INFO @ Sat, 11 Dec 2021 15:06:52: end of X-cor INFO @ Sat, 11 Dec 2021 15:06:52: #2 finished! INFO @ Sat, 11 Dec 2021 15:06:52: #2 predicted fragment length is 248 bps INFO @ Sat, 11 Dec 2021 15:06:52: #2 alternative fragment length(s) may be 248 bps INFO @ Sat, 11 Dec 2021 15:06:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7889141/SRX7889141.20_model.r INFO @ Sat, 11 Dec 2021 15:06:52: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:06:52: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:07:17: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:07:17: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:07:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7889141/SRX7889141.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:07:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7889141/SRX7889141.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:07:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7889141/SRX7889141.20_summits.bed INFO @ Sat, 11 Dec 2021 15:07:30: Done! INFO @ Sat, 11 Dec 2021 15:07:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7889141/SRX7889141.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:07:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7889141/SRX7889141.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:07:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7889141/SRX7889141.10_summits.bed INFO @ Sat, 11 Dec 2021 15:07:31: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1554 records, 4 fields): 19 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3182 records, 4 fields): 4 millis CompletedMACS2peakCalling