Job ID = 14172337 SRX = SRX7628879 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 20887663 spots for SRR10963241/SRR10963241.sra Written 20887663 spots for SRR10963241/SRR10963241.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172954 ("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: 00:38:53 20887663 reads; of these: 20887663 (100.00%) were paired; of these: 1040929 (4.98%) aligned concordantly 0 times 13920469 (66.64%) aligned concordantly exactly 1 time 5926265 (28.37%) aligned concordantly >1 times ---- 1040929 pairs aligned concordantly 0 times; of these: 44684 (4.29%) aligned discordantly 1 time ---- 996245 pairs aligned 0 times concordantly or discordantly; of these: 1992490 mates make up the pairs; of these: 1206980 (60.58%) aligned 0 times 485935 (24.39%) aligned exactly 1 time 299575 (15.04%) aligned >1 times 97.11% overall alignment rate Time searching: 00:38:53 Overall time: 00:38:53 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_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] 879026 / 19875901 = 0.0442 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 15:57:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628879/SRX7628879.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628879/SRX7628879.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628879/SRX7628879.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628879/SRX7628879.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 15:57:31: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:57:31: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:57:36: 1000000 INFO @ Sat, 11 Dec 2021 15:57:41: 2000000 INFO @ Sat, 11 Dec 2021 15:57:45: 3000000 INFO @ Sat, 11 Dec 2021 15:57:50: 4000000 INFO @ Sat, 11 Dec 2021 15:57:55: 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 15:58:00: 6000000 INFO @ Sat, 11 Dec 2021 15:58:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628879/SRX7628879.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628879/SRX7628879.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628879/SRX7628879.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628879/SRX7628879.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 15:58:01: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:58:01: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:58:05: 7000000 INFO @ Sat, 11 Dec 2021 15:58:05: 1000000 INFO @ Sat, 11 Dec 2021 15:58:10: 8000000 INFO @ Sat, 11 Dec 2021 15:58:10: 2000000 INFO @ Sat, 11 Dec 2021 15:58:14: 3000000 INFO @ Sat, 11 Dec 2021 15:58:15: 9000000 INFO @ Sat, 11 Dec 2021 15:58:19: 4000000 INFO @ Sat, 11 Dec 2021 15:58:20: 10000000 INFO @ Sat, 11 Dec 2021 15:58:23: 5000000 INFO @ Sat, 11 Dec 2021 15:58:24: 11000000 INFO @ Sat, 11 Dec 2021 15:58:28: 6000000 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 15:58:29: 12000000 INFO @ Sat, 11 Dec 2021 15:58:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628879/SRX7628879.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628879/SRX7628879.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628879/SRX7628879.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628879/SRX7628879.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 15:58:31: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:58:31: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:58:32: 7000000 INFO @ Sat, 11 Dec 2021 15:58:34: 13000000 INFO @ Sat, 11 Dec 2021 15:58:35: 1000000 INFO @ Sat, 11 Dec 2021 15:58:36: 8000000 INFO @ Sat, 11 Dec 2021 15:58:39: 14000000 INFO @ Sat, 11 Dec 2021 15:58:40: 2000000 INFO @ Sat, 11 Dec 2021 15:58:41: 9000000 INFO @ Sat, 11 Dec 2021 15:58:44: 15000000 INFO @ Sat, 11 Dec 2021 15:58:44: 3000000 INFO @ Sat, 11 Dec 2021 15:58:45: 10000000 INFO @ Sat, 11 Dec 2021 15:58:49: 4000000 INFO @ Sat, 11 Dec 2021 15:58:49: 16000000 INFO @ Sat, 11 Dec 2021 15:58:50: 11000000 INFO @ Sat, 11 Dec 2021 15:58:53: 5000000 INFO @ Sat, 11 Dec 2021 15:58:54: 12000000 INFO @ Sat, 11 Dec 2021 15:58:54: 17000000 INFO @ Sat, 11 Dec 2021 15:58:58: 6000000 INFO @ Sat, 11 Dec 2021 15:58:59: 13000000 INFO @ Sat, 11 Dec 2021 15:58:59: 18000000 INFO @ Sat, 11 Dec 2021 15:59:02: 7000000 INFO @ Sat, 11 Dec 2021 15:59:03: 14000000 INFO @ Sat, 11 Dec 2021 15:59:04: 19000000 INFO @ Sat, 11 Dec 2021 15:59:07: 8000000 INFO @ Sat, 11 Dec 2021 15:59:07: 15000000 INFO @ Sat, 11 Dec 2021 15:59:09: 20000000 INFO @ Sat, 11 Dec 2021 15:59:11: 9000000 INFO @ Sat, 11 Dec 2021 15:59:12: 16000000 INFO @ Sat, 11 Dec 2021 15:59:14: 21000000 INFO @ Sat, 11 Dec 2021 15:59:15: 10000000 INFO @ Sat, 11 Dec 2021 15:59:16: 17000000 INFO @ Sat, 11 Dec 2021 15:59:19: 22000000 INFO @ Sat, 11 Dec 2021 15:59:20: 11000000 INFO @ Sat, 11 Dec 2021 15:59:21: 18000000 INFO @ Sat, 11 Dec 2021 15:59:24: 23000000 INFO @ Sat, 11 Dec 2021 15:59:24: 12000000 INFO @ Sat, 11 Dec 2021 15:59:25: 19000000 INFO @ Sat, 11 Dec 2021 15:59:29: 13000000 INFO @ Sat, 11 Dec 2021 15:59:29: 24000000 INFO @ Sat, 11 Dec 2021 15:59:30: 20000000 INFO @ Sat, 11 Dec 2021 15:59:33: 14000000 INFO @ Sat, 11 Dec 2021 15:59:34: 25000000 INFO @ Sat, 11 Dec 2021 15:59:34: 21000000 INFO @ Sat, 11 Dec 2021 15:59:37: 15000000 INFO @ Sat, 11 Dec 2021 15:59:38: 22000000 INFO @ Sat, 11 Dec 2021 15:59:39: 26000000 INFO @ Sat, 11 Dec 2021 15:59:42: 16000000 INFO @ Sat, 11 Dec 2021 15:59:43: 23000000 INFO @ Sat, 11 Dec 2021 15:59:44: 27000000 INFO @ Sat, 11 Dec 2021 15:59:46: 17000000 INFO @ Sat, 11 Dec 2021 15:59:47: 24000000 INFO @ Sat, 11 Dec 2021 15:59:49: 28000000 INFO @ Sat, 11 Dec 2021 15:59:51: 18000000 INFO @ Sat, 11 Dec 2021 15:59:52: 25000000 INFO @ Sat, 11 Dec 2021 15:59:54: 29000000 INFO @ Sat, 11 Dec 2021 15:59:55: 19000000 INFO @ Sat, 11 Dec 2021 15:59:56: 26000000 INFO @ Sat, 11 Dec 2021 15:59:59: 30000000 INFO @ Sat, 11 Dec 2021 15:59:59: 20000000 INFO @ Sat, 11 Dec 2021 16:00:00: 27000000 INFO @ Sat, 11 Dec 2021 16:00:04: 21000000 INFO @ Sat, 11 Dec 2021 16:00:04: 31000000 INFO @ Sat, 11 Dec 2021 16:00:05: 28000000 INFO @ Sat, 11 Dec 2021 16:00:08: 22000000 INFO @ Sat, 11 Dec 2021 16:00:09: 32000000 INFO @ Sat, 11 Dec 2021 16:00:09: 29000000 INFO @ Sat, 11 Dec 2021 16:00:13: 23000000 INFO @ Sat, 11 Dec 2021 16:00:14: 30000000 INFO @ Sat, 11 Dec 2021 16:00:14: 33000000 INFO @ Sat, 11 Dec 2021 16:00:17: 24000000 INFO @ Sat, 11 Dec 2021 16:00:18: 31000000 INFO @ Sat, 11 Dec 2021 16:00:19: 34000000 INFO @ Sat, 11 Dec 2021 16:00:21: 25000000 INFO @ Sat, 11 Dec 2021 16:00:23: 32000000 INFO @ Sat, 11 Dec 2021 16:00:24: 35000000 INFO @ Sat, 11 Dec 2021 16:00:26: 26000000 INFO @ Sat, 11 Dec 2021 16:00:27: 33000000 INFO @ Sat, 11 Dec 2021 16:00:29: 36000000 INFO @ Sat, 11 Dec 2021 16:00:30: 27000000 INFO @ Sat, 11 Dec 2021 16:00:31: 34000000 INFO @ Sat, 11 Dec 2021 16:00:34: 37000000 INFO @ Sat, 11 Dec 2021 16:00:35: 28000000 INFO @ Sat, 11 Dec 2021 16:00:36: 35000000 INFO @ Sat, 11 Dec 2021 16:00:39: 38000000 INFO @ Sat, 11 Dec 2021 16:00:39: 29000000 INFO @ Sat, 11 Dec 2021 16:00:40: 36000000 INFO @ Sat, 11 Dec 2021 16:00:43: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 16:00:43: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 16:00:43: #1 total tags in treatment: 18968592 INFO @ Sat, 11 Dec 2021 16:00:43: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:00:43: #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 16:00:43: #1 tags after filtering in treatment: 17301265 INFO @ Sat, 11 Dec 2021 16:00:43: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 11 Dec 2021 16:00:43: #1 finished! INFO @ Sat, 11 Dec 2021 16:00:43: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:00:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:00:43: 30000000 INFO @ Sat, 11 Dec 2021 16:00:44: #2 number of paired peaks: 771 WARNING @ Sat, 11 Dec 2021 16:00:44: Fewer paired peaks (771) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 771 pairs to build model! INFO @ Sat, 11 Dec 2021 16:00:44: start model_add_line... INFO @ Sat, 11 Dec 2021 16:00:45: start X-correlation... INFO @ Sat, 11 Dec 2021 16:00:45: 37000000 INFO @ Sat, 11 Dec 2021 16:00:45: end of X-cor INFO @ Sat, 11 Dec 2021 16:00:45: #2 finished! INFO @ Sat, 11 Dec 2021 16:00:45: #2 predicted fragment length is 124 bps INFO @ Sat, 11 Dec 2021 16:00:45: #2 alternative fragment length(s) may be 4,124 bps INFO @ Sat, 11 Dec 2021 16:00:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628879/SRX7628879.05_model.r INFO @ Sat, 11 Dec 2021 16:00:45: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:00:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:00:48: 31000000 INFO @ Sat, 11 Dec 2021 16:00:49: 38000000 INFO @ Sat, 11 Dec 2021 16:00:52: 32000000 INFO @ Sat, 11 Dec 2021 16:00:53: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 16:00:53: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 16:00:53: #1 total tags in treatment: 18968592 INFO @ Sat, 11 Dec 2021 16:00:53: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:00:53: #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 16:00:53: #1 tags after filtering in treatment: 17301265 INFO @ Sat, 11 Dec 2021 16:00:53: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 11 Dec 2021 16:00:53: #1 finished! INFO @ Sat, 11 Dec 2021 16:00:53: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:00:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:00:54: #2 number of paired peaks: 771 WARNING @ Sat, 11 Dec 2021 16:00:54: Fewer paired peaks (771) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 771 pairs to build model! INFO @ Sat, 11 Dec 2021 16:00:54: start model_add_line... INFO @ Sat, 11 Dec 2021 16:00:54: start X-correlation... INFO @ Sat, 11 Dec 2021 16:00:54: end of X-cor INFO @ Sat, 11 Dec 2021 16:00:54: #2 finished! INFO @ Sat, 11 Dec 2021 16:00:54: #2 predicted fragment length is 124 bps INFO @ Sat, 11 Dec 2021 16:00:54: #2 alternative fragment length(s) may be 4,124 bps INFO @ Sat, 11 Dec 2021 16:00:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628879/SRX7628879.10_model.r INFO @ Sat, 11 Dec 2021 16:00:54: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:00:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:00:56: 33000000 INFO @ Sat, 11 Dec 2021 16:01:01: 34000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 16:01:05: 35000000 INFO @ Sat, 11 Dec 2021 16:01:09: 36000000 INFO @ Sat, 11 Dec 2021 16:01:13: 37000000 INFO @ Sat, 11 Dec 2021 16:01:17: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:01:18: 38000000 INFO @ Sat, 11 Dec 2021 16:01:21: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 16:01:21: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 16:01:21: #1 total tags in treatment: 18968592 INFO @ Sat, 11 Dec 2021 16:01:21: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:01:21: #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 16:01:22: #1 tags after filtering in treatment: 17301265 INFO @ Sat, 11 Dec 2021 16:01:22: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 11 Dec 2021 16:01:22: #1 finished! INFO @ Sat, 11 Dec 2021 16:01:22: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:01:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:01:23: #2 number of paired peaks: 771 WARNING @ Sat, 11 Dec 2021 16:01:23: Fewer paired peaks (771) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 771 pairs to build model! INFO @ Sat, 11 Dec 2021 16:01:23: start model_add_line... INFO @ Sat, 11 Dec 2021 16:01:23: start X-correlation... INFO @ Sat, 11 Dec 2021 16:01:23: end of X-cor INFO @ Sat, 11 Dec 2021 16:01:23: #2 finished! INFO @ Sat, 11 Dec 2021 16:01:23: #2 predicted fragment length is 124 bps INFO @ Sat, 11 Dec 2021 16:01:23: #2 alternative fragment length(s) may be 4,124 bps INFO @ Sat, 11 Dec 2021 16:01:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628879/SRX7628879.20_model.r INFO @ Sat, 11 Dec 2021 16:01:23: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:01:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:01:27: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:01:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628879/SRX7628879.05_peaks.xls INFO @ Sat, 11 Dec 2021 16:01:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628879/SRX7628879.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:01:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628879/SRX7628879.05_summits.bed INFO @ Sat, 11 Dec 2021 16:01:32: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7137 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:01:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628879/SRX7628879.10_peaks.xls INFO @ Sat, 11 Dec 2021 16:01:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628879/SRX7628879.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:01:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628879/SRX7628879.10_summits.bed INFO @ Sat, 11 Dec 2021 16:01:42: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3668 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:01:55: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:02:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628879/SRX7628879.20_peaks.xls INFO @ Sat, 11 Dec 2021 16:02:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628879/SRX7628879.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:02:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628879/SRX7628879.20_summits.bed INFO @ Sat, 11 Dec 2021 16:02:11: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1291 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。