Job ID = 14172415 SRX = SRX7628880 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18954496 spots for SRR10963242/SRR10963242.sra Written 18954496 spots for SRR10963242/SRR10963242.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172994 ("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: 00:35:48 18954496 reads; of these: 18954496 (100.00%) were paired; of these: 973291 (5.13%) aligned concordantly 0 times 12592239 (66.43%) aligned concordantly exactly 1 time 5388966 (28.43%) aligned concordantly >1 times ---- 973291 pairs aligned concordantly 0 times; of these: 36857 (3.79%) aligned discordantly 1 time ---- 936434 pairs aligned 0 times concordantly or discordantly; of these: 1872868 mates make up the pairs; of these: 1132294 (60.46%) aligned 0 times 444254 (23.72%) aligned exactly 1 time 296320 (15.82%) aligned >1 times 97.01% overall alignment rate Time searching: 00:35:48 Overall time: 00:35:48 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] 809881 / 18005827 = 0.0450 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 16:04:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628880/SRX7628880.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628880/SRX7628880.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628880/SRX7628880.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628880/SRX7628880.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 16:04:29: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:04:29: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:04:33: 1000000 INFO @ Sat, 11 Dec 2021 16:04:37: 2000000 INFO @ Sat, 11 Dec 2021 16:04:42: 3000000 INFO @ Sat, 11 Dec 2021 16:04:46: 4000000 INFO @ Sat, 11 Dec 2021 16:04:50: 5000000 INFO @ Sat, 11 Dec 2021 16:04:54: 6000000 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 16:04:58: 7000000 INFO @ Sat, 11 Dec 2021 16:04:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628880/SRX7628880.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628880/SRX7628880.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628880/SRX7628880.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628880/SRX7628880.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 16:04:59: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:04:59: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:05:02: 8000000 INFO @ Sat, 11 Dec 2021 16:05:04: 1000000 INFO @ Sat, 11 Dec 2021 16:05:06: 9000000 INFO @ Sat, 11 Dec 2021 16:05:08: 2000000 INFO @ Sat, 11 Dec 2021 16:05:10: 10000000 INFO @ Sat, 11 Dec 2021 16:05:13: 3000000 INFO @ Sat, 11 Dec 2021 16:05:14: 11000000 INFO @ Sat, 11 Dec 2021 16:05:18: 4000000 INFO @ Sat, 11 Dec 2021 16:05:19: 12000000 INFO @ Sat, 11 Dec 2021 16:05:23: 13000000 INFO @ Sat, 11 Dec 2021 16:05:23: 5000000 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 16:05:27: 14000000 INFO @ Sat, 11 Dec 2021 16:05:28: 6000000 INFO @ Sat, 11 Dec 2021 16:05:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628880/SRX7628880.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628880/SRX7628880.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628880/SRX7628880.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628880/SRX7628880.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 16:05:29: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:05:29: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:05:31: 15000000 INFO @ Sat, 11 Dec 2021 16:05:33: 1000000 INFO @ Sat, 11 Dec 2021 16:05:33: 7000000 INFO @ Sat, 11 Dec 2021 16:05:35: 16000000 INFO @ Sat, 11 Dec 2021 16:05:37: 2000000 INFO @ Sat, 11 Dec 2021 16:05:38: 8000000 INFO @ Sat, 11 Dec 2021 16:05:40: 17000000 INFO @ Sat, 11 Dec 2021 16:05:42: 3000000 INFO @ Sat, 11 Dec 2021 16:05:43: 9000000 INFO @ Sat, 11 Dec 2021 16:05:44: 18000000 INFO @ Sat, 11 Dec 2021 16:05:46: 4000000 INFO @ Sat, 11 Dec 2021 16:05:48: 10000000 INFO @ Sat, 11 Dec 2021 16:05:48: 19000000 INFO @ Sat, 11 Dec 2021 16:05:50: 5000000 INFO @ Sat, 11 Dec 2021 16:05:52: 20000000 INFO @ Sat, 11 Dec 2021 16:05:53: 11000000 INFO @ Sat, 11 Dec 2021 16:05:54: 6000000 INFO @ Sat, 11 Dec 2021 16:05:57: 21000000 INFO @ Sat, 11 Dec 2021 16:05:58: 12000000 INFO @ Sat, 11 Dec 2021 16:05:58: 7000000 INFO @ Sat, 11 Dec 2021 16:06:01: 22000000 INFO @ Sat, 11 Dec 2021 16:06:03: 8000000 INFO @ Sat, 11 Dec 2021 16:06:03: 13000000 INFO @ Sat, 11 Dec 2021 16:06:05: 23000000 INFO @ Sat, 11 Dec 2021 16:06:07: 9000000 INFO @ Sat, 11 Dec 2021 16:06:08: 14000000 INFO @ Sat, 11 Dec 2021 16:06:09: 24000000 INFO @ Sat, 11 Dec 2021 16:06:11: 10000000 INFO @ Sat, 11 Dec 2021 16:06:13: 15000000 INFO @ Sat, 11 Dec 2021 16:06:13: 25000000 INFO @ Sat, 11 Dec 2021 16:06:15: 11000000 INFO @ Sat, 11 Dec 2021 16:06:18: 26000000 INFO @ Sat, 11 Dec 2021 16:06:18: 16000000 INFO @ Sat, 11 Dec 2021 16:06:19: 12000000 INFO @ Sat, 11 Dec 2021 16:06:22: 27000000 INFO @ Sat, 11 Dec 2021 16:06:23: 17000000 INFO @ Sat, 11 Dec 2021 16:06:23: 13000000 INFO @ Sat, 11 Dec 2021 16:06:26: 28000000 INFO @ Sat, 11 Dec 2021 16:06:28: 14000000 INFO @ Sat, 11 Dec 2021 16:06:28: 18000000 INFO @ Sat, 11 Dec 2021 16:06:31: 29000000 INFO @ Sat, 11 Dec 2021 16:06:32: 15000000 INFO @ Sat, 11 Dec 2021 16:06:33: 19000000 INFO @ Sat, 11 Dec 2021 16:06:35: 30000000 INFO @ Sat, 11 Dec 2021 16:06:36: 16000000 INFO @ Sat, 11 Dec 2021 16:06:38: 20000000 INFO @ Sat, 11 Dec 2021 16:06:39: 31000000 INFO @ Sat, 11 Dec 2021 16:06:40: 17000000 INFO @ Sat, 11 Dec 2021 16:06:43: 21000000 INFO @ Sat, 11 Dec 2021 16:06:43: 32000000 INFO @ Sat, 11 Dec 2021 16:06:45: 18000000 INFO @ Sat, 11 Dec 2021 16:06:48: 33000000 INFO @ Sat, 11 Dec 2021 16:06:48: 22000000 INFO @ Sat, 11 Dec 2021 16:06:49: 19000000 INFO @ Sat, 11 Dec 2021 16:06:52: 34000000 INFO @ Sat, 11 Dec 2021 16:06:53: 20000000 INFO @ Sat, 11 Dec 2021 16:06:53: 23000000 INFO @ Sat, 11 Dec 2021 16:06:56: 35000000 INFO @ Sat, 11 Dec 2021 16:06:57: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 16:06:57: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 16:06:57: #1 total tags in treatment: 17172128 INFO @ Sat, 11 Dec 2021 16:06:57: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:06:57: #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 16:06:57: #1 tags after filtering in treatment: 15757345 INFO @ Sat, 11 Dec 2021 16:06:57: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 11 Dec 2021 16:06:57: #1 finished! INFO @ Sat, 11 Dec 2021 16:06:57: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:06:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:06:57: 21000000 INFO @ Sat, 11 Dec 2021 16:06:58: #2 number of paired peaks: 819 WARNING @ Sat, 11 Dec 2021 16:06:58: Fewer paired peaks (819) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 819 pairs to build model! INFO @ Sat, 11 Dec 2021 16:06:58: start model_add_line... INFO @ Sat, 11 Dec 2021 16:06:58: start X-correlation... INFO @ Sat, 11 Dec 2021 16:06:58: end of X-cor INFO @ Sat, 11 Dec 2021 16:06:58: #2 finished! INFO @ Sat, 11 Dec 2021 16:06:58: #2 predicted fragment length is 133 bps INFO @ Sat, 11 Dec 2021 16:06:58: #2 alternative fragment length(s) may be 133 bps INFO @ Sat, 11 Dec 2021 16:06:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628880/SRX7628880.05_model.r INFO @ Sat, 11 Dec 2021 16:06:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:06:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:06:59: 24000000 INFO @ Sat, 11 Dec 2021 16:07:01: 22000000 INFO @ Sat, 11 Dec 2021 16:07:04: 25000000 INFO @ Sat, 11 Dec 2021 16:07:06: 23000000 INFO @ Sat, 11 Dec 2021 16:07:09: 26000000 INFO @ Sat, 11 Dec 2021 16:07:10: 24000000 INFO @ Sat, 11 Dec 2021 16:07:14: 27000000 INFO @ Sat, 11 Dec 2021 16:07:14: 25000000 INFO @ Sat, 11 Dec 2021 16:07:18: 26000000 INFO @ Sat, 11 Dec 2021 16:07:19: 28000000 INFO @ Sat, 11 Dec 2021 16:07:22: 27000000 INFO @ Sat, 11 Dec 2021 16:07:24: 29000000 INFO @ Sat, 11 Dec 2021 16:07:27: 28000000 INFO @ Sat, 11 Dec 2021 16:07:29: 30000000 INFO @ Sat, 11 Dec 2021 16:07:31: 29000000 INFO @ Sat, 11 Dec 2021 16:07:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:07:34: 31000000 INFO @ Sat, 11 Dec 2021 16:07:35: 30000000 INFO @ Sat, 11 Dec 2021 16:07:39: 32000000 INFO @ Sat, 11 Dec 2021 16:07:39: 31000000 INFO @ Sat, 11 Dec 2021 16:07:43: 32000000 INFO @ Sat, 11 Dec 2021 16:07:43: 33000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 16:07:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628880/SRX7628880.05_peaks.xls INFO @ Sat, 11 Dec 2021 16:07:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628880/SRX7628880.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:07:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628880/SRX7628880.05_summits.bed INFO @ Sat, 11 Dec 2021 16:07:46: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6817 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:07:47: 33000000 INFO @ Sat, 11 Dec 2021 16:07:48: 34000000 INFO @ Sat, 11 Dec 2021 16:07:52: 34000000 INFO @ Sat, 11 Dec 2021 16:07:54: 35000000 INFO @ Sat, 11 Dec 2021 16:07:54: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 16:07:54: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 16:07:54: #1 total tags in treatment: 17172128 INFO @ Sat, 11 Dec 2021 16:07:54: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:07:54: #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 16:07:55: #1 tags after filtering in treatment: 15757345 INFO @ Sat, 11 Dec 2021 16:07:55: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 11 Dec 2021 16:07:55: #1 finished! INFO @ Sat, 11 Dec 2021 16:07:55: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:07:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:07:56: #2 number of paired peaks: 819 WARNING @ Sat, 11 Dec 2021 16:07:56: Fewer paired peaks (819) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 819 pairs to build model! INFO @ Sat, 11 Dec 2021 16:07:56: start model_add_line... INFO @ Sat, 11 Dec 2021 16:07:56: start X-correlation... INFO @ Sat, 11 Dec 2021 16:07:56: end of X-cor INFO @ Sat, 11 Dec 2021 16:07:56: #2 finished! INFO @ Sat, 11 Dec 2021 16:07:56: #2 predicted fragment length is 133 bps INFO @ Sat, 11 Dec 2021 16:07:56: #2 alternative fragment length(s) may be 133 bps INFO @ Sat, 11 Dec 2021 16:07:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628880/SRX7628880.10_model.r INFO @ Sat, 11 Dec 2021 16:07:56: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:07:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:07:56: 35000000 INFO @ Sat, 11 Dec 2021 16:07:57: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 16:07:57: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 16:07:57: #1 total tags in treatment: 17172128 INFO @ Sat, 11 Dec 2021 16:07:57: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:07:57: #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 16:07:57: #1 tags after filtering in treatment: 15757345 INFO @ Sat, 11 Dec 2021 16:07:57: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 11 Dec 2021 16:07:57: #1 finished! INFO @ Sat, 11 Dec 2021 16:07:57: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:07:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:07:58: #2 number of paired peaks: 819 WARNING @ Sat, 11 Dec 2021 16:07:58: Fewer paired peaks (819) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 819 pairs to build model! INFO @ Sat, 11 Dec 2021 16:07:58: start model_add_line... INFO @ Sat, 11 Dec 2021 16:07:58: start X-correlation... INFO @ Sat, 11 Dec 2021 16:07:58: end of X-cor INFO @ Sat, 11 Dec 2021 16:07:58: #2 finished! INFO @ Sat, 11 Dec 2021 16:07:58: #2 predicted fragment length is 133 bps INFO @ Sat, 11 Dec 2021 16:07:58: #2 alternative fragment length(s) may be 133 bps INFO @ Sat, 11 Dec 2021 16:07:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628880/SRX7628880.20_model.r INFO @ Sat, 11 Dec 2021 16:07:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:07:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:08:27: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:08:28: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:08:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628880/SRX7628880.20_peaks.xls INFO @ Sat, 11 Dec 2021 16:08:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628880/SRX7628880.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:08:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628880/SRX7628880.20_summits.bed INFO @ Sat, 11 Dec 2021 16:08:42: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1216 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:08:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628880/SRX7628880.10_peaks.xls INFO @ Sat, 11 Dec 2021 16:08:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628880/SRX7628880.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:08:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628880/SRX7628880.10_summits.bed INFO @ Sat, 11 Dec 2021 16:08:42: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3506 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。