Job ID = 14168116 SRX = ERX3978944 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 58934631 spots for ERR3976014/ERR3976014.sra Written 58934631 spots for ERR3976014/ERR3976014.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169606 ("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: 03:06:33 58934631 reads; of these: 58934631 (100.00%) were paired; of these: 7718104 (13.10%) aligned concordantly 0 times 37942366 (64.38%) aligned concordantly exactly 1 time 13274161 (22.52%) aligned concordantly >1 times ---- 7718104 pairs aligned concordantly 0 times; of these: 809901 (10.49%) aligned discordantly 1 time ---- 6908203 pairs aligned 0 times concordantly or discordantly; of these: 13816406 mates make up the pairs; of these: 6283517 (45.48%) aligned 0 times 3348779 (24.24%) aligned exactly 1 time 4184110 (30.28%) aligned >1 times 94.67% overall alignment rate Time searching: 03:06:33 Overall time: 03:06:33 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 48 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] 35264986 / 51704398 = 0.6821 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 19:04:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978944/ERX3978944.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978944/ERX3978944.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978944/ERX3978944.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978944/ERX3978944.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 19:04:09: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:04:09: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:04:14: 1000000 INFO @ Fri, 10 Dec 2021 19:04:19: 2000000 INFO @ Fri, 10 Dec 2021 19:04:24: 3000000 INFO @ Fri, 10 Dec 2021 19:04:28: 4000000 INFO @ Fri, 10 Dec 2021 19:04:33: 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 19:04:37: 6000000 INFO @ Fri, 10 Dec 2021 19:04:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978944/ERX3978944.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978944/ERX3978944.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978944/ERX3978944.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978944/ERX3978944.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 19:04:38: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:04:38: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:04:42: 7000000 INFO @ Fri, 10 Dec 2021 19:04:44: 1000000 INFO @ Fri, 10 Dec 2021 19:04:47: 8000000 INFO @ Fri, 10 Dec 2021 19:04:49: 2000000 INFO @ Fri, 10 Dec 2021 19:04:51: 9000000 INFO @ Fri, 10 Dec 2021 19:04:54: 3000000 INFO @ Fri, 10 Dec 2021 19:04:56: 10000000 INFO @ Fri, 10 Dec 2021 19:04:59: 4000000 INFO @ Fri, 10 Dec 2021 19:05:01: 11000000 INFO @ Fri, 10 Dec 2021 19:05:04: 5000000 INFO @ Fri, 10 Dec 2021 19:05:06: 12000000 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 19:05:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978944/ERX3978944.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978944/ERX3978944.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978944/ERX3978944.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978944/ERX3978944.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 19:05:08: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:05:08: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:05:09: 6000000 INFO @ Fri, 10 Dec 2021 19:05:11: 13000000 INFO @ Fri, 10 Dec 2021 19:05:13: 1000000 INFO @ Fri, 10 Dec 2021 19:05:14: 7000000 INFO @ Fri, 10 Dec 2021 19:05:15: 14000000 INFO @ Fri, 10 Dec 2021 19:05:19: 8000000 INFO @ Fri, 10 Dec 2021 19:05:19: 2000000 INFO @ Fri, 10 Dec 2021 19:05:20: 15000000 INFO @ Fri, 10 Dec 2021 19:05:24: 9000000 INFO @ Fri, 10 Dec 2021 19:05:25: 3000000 INFO @ Fri, 10 Dec 2021 19:05:25: 16000000 INFO @ Fri, 10 Dec 2021 19:05:28: 10000000 INFO @ Fri, 10 Dec 2021 19:05:30: 17000000 INFO @ Fri, 10 Dec 2021 19:05:30: 4000000 INFO @ Fri, 10 Dec 2021 19:05:33: 11000000 INFO @ Fri, 10 Dec 2021 19:05:35: 18000000 INFO @ Fri, 10 Dec 2021 19:05:36: 5000000 INFO @ Fri, 10 Dec 2021 19:05:38: 12000000 INFO @ Fri, 10 Dec 2021 19:05:39: 19000000 INFO @ Fri, 10 Dec 2021 19:05:42: 6000000 INFO @ Fri, 10 Dec 2021 19:05:43: 13000000 INFO @ Fri, 10 Dec 2021 19:05:44: 20000000 INFO @ Fri, 10 Dec 2021 19:05:47: 7000000 INFO @ Fri, 10 Dec 2021 19:05:48: 14000000 INFO @ Fri, 10 Dec 2021 19:05:49: 21000000 INFO @ Fri, 10 Dec 2021 19:05:53: 15000000 INFO @ Fri, 10 Dec 2021 19:05:53: 8000000 INFO @ Fri, 10 Dec 2021 19:05:54: 22000000 INFO @ Fri, 10 Dec 2021 19:05:58: 16000000 INFO @ Fri, 10 Dec 2021 19:05:59: 23000000 INFO @ Fri, 10 Dec 2021 19:05:59: 9000000 INFO @ Fri, 10 Dec 2021 19:06:02: 17000000 INFO @ Fri, 10 Dec 2021 19:06:04: 24000000 INFO @ Fri, 10 Dec 2021 19:06:04: 10000000 INFO @ Fri, 10 Dec 2021 19:06:07: 18000000 INFO @ Fri, 10 Dec 2021 19:06:09: 25000000 INFO @ Fri, 10 Dec 2021 19:06:10: 11000000 INFO @ Fri, 10 Dec 2021 19:06:12: 19000000 INFO @ Fri, 10 Dec 2021 19:06:13: 26000000 INFO @ Fri, 10 Dec 2021 19:06:16: 12000000 INFO @ Fri, 10 Dec 2021 19:06:17: 20000000 INFO @ Fri, 10 Dec 2021 19:06:18: 27000000 INFO @ Fri, 10 Dec 2021 19:06:22: 21000000 INFO @ Fri, 10 Dec 2021 19:06:22: 13000000 INFO @ Fri, 10 Dec 2021 19:06:23: 28000000 INFO @ Fri, 10 Dec 2021 19:06:27: 22000000 INFO @ Fri, 10 Dec 2021 19:06:27: 14000000 INFO @ Fri, 10 Dec 2021 19:06:28: 29000000 INFO @ Fri, 10 Dec 2021 19:06:32: 23000000 INFO @ Fri, 10 Dec 2021 19:06:33: 15000000 INFO @ Fri, 10 Dec 2021 19:06:33: 30000000 INFO @ Fri, 10 Dec 2021 19:06:37: 24000000 INFO @ Fri, 10 Dec 2021 19:06:38: 31000000 INFO @ Fri, 10 Dec 2021 19:06:39: 16000000 INFO @ Fri, 10 Dec 2021 19:06:42: 25000000 INFO @ Fri, 10 Dec 2021 19:06:43: 32000000 INFO @ Fri, 10 Dec 2021 19:06:45: 17000000 INFO @ Fri, 10 Dec 2021 19:06:47: 26000000 INFO @ Fri, 10 Dec 2021 19:06:48: 33000000 INFO @ Fri, 10 Dec 2021 19:06:50: 18000000 INFO @ Fri, 10 Dec 2021 19:06:52: 27000000 INFO @ Fri, 10 Dec 2021 19:06:53: 34000000 INFO @ Fri, 10 Dec 2021 19:06:56: 19000000 INFO @ Fri, 10 Dec 2021 19:06:56: 28000000 INFO @ Fri, 10 Dec 2021 19:06:58: 35000000 INFO @ Fri, 10 Dec 2021 19:07:01: 29000000 INFO @ Fri, 10 Dec 2021 19:07:01: 20000000 INFO @ Fri, 10 Dec 2021 19:07:03: 36000000 INFO @ Fri, 10 Dec 2021 19:07:06: 30000000 INFO @ Fri, 10 Dec 2021 19:07:07: 21000000 INFO @ Fri, 10 Dec 2021 19:07:08: 37000000 INFO @ Fri, 10 Dec 2021 19:07:12: 31000000 INFO @ Fri, 10 Dec 2021 19:07:13: 38000000 INFO @ Fri, 10 Dec 2021 19:07:13: 22000000 INFO @ Fri, 10 Dec 2021 19:07:17: 32000000 INFO @ Fri, 10 Dec 2021 19:07:18: 39000000 INFO @ Fri, 10 Dec 2021 19:07:19: 23000000 INFO @ Fri, 10 Dec 2021 19:07:21: 33000000 INFO @ Fri, 10 Dec 2021 19:07:23: 40000000 INFO @ Fri, 10 Dec 2021 19:07:25: 24000000 INFO @ Fri, 10 Dec 2021 19:07:26: 34000000 INFO @ Fri, 10 Dec 2021 19:07:27: 41000000 INFO @ Fri, 10 Dec 2021 19:07:28: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 19:07:28: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 19:07:28: #1 total tags in treatment: 16390582 INFO @ Fri, 10 Dec 2021 19:07:28: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:07:28: #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 19:07:28: #1 tags after filtering in treatment: 14451991 INFO @ Fri, 10 Dec 2021 19:07:28: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 10 Dec 2021 19:07:28: #1 finished! INFO @ Fri, 10 Dec 2021 19:07:28: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:07:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:07:29: #2 number of paired peaks: 729 WARNING @ Fri, 10 Dec 2021 19:07:29: Fewer paired peaks (729) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 729 pairs to build model! INFO @ Fri, 10 Dec 2021 19:07:29: start model_add_line... INFO @ Fri, 10 Dec 2021 19:07:29: start X-correlation... INFO @ Fri, 10 Dec 2021 19:07:29: end of X-cor INFO @ Fri, 10 Dec 2021 19:07:29: #2 finished! INFO @ Fri, 10 Dec 2021 19:07:29: #2 predicted fragment length is 160 bps INFO @ Fri, 10 Dec 2021 19:07:29: #2 alternative fragment length(s) may be 160 bps INFO @ Fri, 10 Dec 2021 19:07:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978944/ERX3978944.05_model.r INFO @ Fri, 10 Dec 2021 19:07:29: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:07:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:07:31: 25000000 INFO @ Fri, 10 Dec 2021 19:07:32: 35000000 INFO @ Fri, 10 Dec 2021 19:07:36: 26000000 INFO @ Fri, 10 Dec 2021 19:07:36: 36000000 INFO @ Fri, 10 Dec 2021 19:07:41: 37000000 INFO @ Fri, 10 Dec 2021 19:07:42: 27000000 INFO @ Fri, 10 Dec 2021 19:07:46: 38000000 INFO @ Fri, 10 Dec 2021 19:07:48: 28000000 INFO @ Fri, 10 Dec 2021 19:07:51: 39000000 INFO @ Fri, 10 Dec 2021 19:07:54: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 19:07:56: 40000000 INFO @ Fri, 10 Dec 2021 19:07:58: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:08:00: 30000000 INFO @ Fri, 10 Dec 2021 19:08:01: 41000000 INFO @ Fri, 10 Dec 2021 19:08:01: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 19:08:01: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 19:08:01: #1 total tags in treatment: 16390582 INFO @ Fri, 10 Dec 2021 19:08:01: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:08:01: #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 19:08:01: #1 tags after filtering in treatment: 14451991 INFO @ Fri, 10 Dec 2021 19:08:01: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 10 Dec 2021 19:08:01: #1 finished! INFO @ Fri, 10 Dec 2021 19:08:01: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:08:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:08:02: #2 number of paired peaks: 729 WARNING @ Fri, 10 Dec 2021 19:08:02: Fewer paired peaks (729) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 729 pairs to build model! INFO @ Fri, 10 Dec 2021 19:08:02: start model_add_line... INFO @ Fri, 10 Dec 2021 19:08:02: start X-correlation... INFO @ Fri, 10 Dec 2021 19:08:02: end of X-cor INFO @ Fri, 10 Dec 2021 19:08:02: #2 finished! INFO @ Fri, 10 Dec 2021 19:08:02: #2 predicted fragment length is 160 bps INFO @ Fri, 10 Dec 2021 19:08:02: #2 alternative fragment length(s) may be 160 bps INFO @ Fri, 10 Dec 2021 19:08:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978944/ERX3978944.10_model.r INFO @ Fri, 10 Dec 2021 19:08:02: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:08:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:08:05: 31000000 INFO @ Fri, 10 Dec 2021 19:08:11: 32000000 INFO @ Fri, 10 Dec 2021 19:08:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978944/ERX3978944.05_peaks.xls INFO @ Fri, 10 Dec 2021 19:08:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978944/ERX3978944.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:08:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978944/ERX3978944.05_summits.bed INFO @ Fri, 10 Dec 2021 19:08:13: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (14898 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:08:17: 33000000 INFO @ Fri, 10 Dec 2021 19:08:22: 34000000 INFO @ Fri, 10 Dec 2021 19:08:28: 35000000 INFO @ Fri, 10 Dec 2021 19:08:30: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:08:33: 36000000 INFO @ Fri, 10 Dec 2021 19:08:39: 37000000 INFO @ Fri, 10 Dec 2021 19:08:44: 38000000 INFO @ Fri, 10 Dec 2021 19:08:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978944/ERX3978944.10_peaks.xls INFO @ Fri, 10 Dec 2021 19:08:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978944/ERX3978944.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:08:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978944/ERX3978944.10_summits.bed INFO @ Fri, 10 Dec 2021 19:08:45: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10401 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:08:50: 39000000 INFO @ Fri, 10 Dec 2021 19:08:55: 40000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 19:09:01: 41000000 INFO @ Fri, 10 Dec 2021 19:09:01: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 19:09:01: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 19:09:01: #1 total tags in treatment: 16390582 INFO @ Fri, 10 Dec 2021 19:09:01: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:09:01: #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 19:09:02: #1 tags after filtering in treatment: 14451991 INFO @ Fri, 10 Dec 2021 19:09:02: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 10 Dec 2021 19:09:02: #1 finished! INFO @ Fri, 10 Dec 2021 19:09:02: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:09:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:09:03: #2 number of paired peaks: 729 WARNING @ Fri, 10 Dec 2021 19:09:03: Fewer paired peaks (729) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 729 pairs to build model! INFO @ Fri, 10 Dec 2021 19:09:03: start model_add_line... INFO @ Fri, 10 Dec 2021 19:09:03: start X-correlation... INFO @ Fri, 10 Dec 2021 19:09:03: end of X-cor INFO @ Fri, 10 Dec 2021 19:09:03: #2 finished! INFO @ Fri, 10 Dec 2021 19:09:03: #2 predicted fragment length is 160 bps INFO @ Fri, 10 Dec 2021 19:09:03: #2 alternative fragment length(s) may be 160 bps INFO @ Fri, 10 Dec 2021 19:09:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978944/ERX3978944.20_model.r INFO @ Fri, 10 Dec 2021 19:09:03: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:09:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:09:31: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:09:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978944/ERX3978944.20_peaks.xls INFO @ Fri, 10 Dec 2021 19:09:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978944/ERX3978944.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:09:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978944/ERX3978944.20_summits.bed INFO @ Fri, 10 Dec 2021 19:09:47: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5853 records, 4 fields): 52 millis CompletedMACS2peakCalling