Job ID = 14171834 SRX = SRX9008840 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13860803 spots for SRR12518312/SRR12518312.sra Written 13860803 spots for SRR12518312/SRR12518312.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172429 ("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: 00:31:43 13860803 reads; of these: 13860803 (100.00%) were paired; of these: 2298003 (16.58%) aligned concordantly 0 times 9270828 (66.89%) aligned concordantly exactly 1 time 2291972 (16.54%) aligned concordantly >1 times ---- 2298003 pairs aligned concordantly 0 times; of these: 913185 (39.74%) aligned discordantly 1 time ---- 1384818 pairs aligned 0 times concordantly or discordantly; of these: 2769636 mates make up the pairs; of these: 1894350 (68.40%) aligned 0 times 409935 (14.80%) aligned exactly 1 time 465351 (16.80%) aligned >1 times 93.17% overall alignment rate Time searching: 00:31:43 Overall time: 00:31:43 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 12 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] 1134130 / 12435917 = 0.0912 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 13:44:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9008840/SRX9008840.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9008840/SRX9008840.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9008840/SRX9008840.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9008840/SRX9008840.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 13:44:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:44:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:44:40: 1000000 INFO @ Sat, 11 Dec 2021 13:44:49: 2000000 INFO @ Sat, 11 Dec 2021 13:44:58: 3000000 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 13:45:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9008840/SRX9008840.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9008840/SRX9008840.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9008840/SRX9008840.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9008840/SRX9008840.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 13:45:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:45:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:45:07: 4000000 INFO @ Sat, 11 Dec 2021 13:45:11: 1000000 INFO @ Sat, 11 Dec 2021 13:45:16: 5000000 INFO @ Sat, 11 Dec 2021 13:45:21: 2000000 INFO @ Sat, 11 Dec 2021 13:45:26: 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 13:45:31: 3000000 INFO @ Sat, 11 Dec 2021 13:45:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9008840/SRX9008840.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9008840/SRX9008840.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9008840/SRX9008840.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9008840/SRX9008840.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 13:45:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:45:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:45:36: 7000000 INFO @ Sat, 11 Dec 2021 13:45:40: 4000000 INFO @ Sat, 11 Dec 2021 13:45:41: 1000000 INFO @ Sat, 11 Dec 2021 13:45:46: 8000000 INFO @ Sat, 11 Dec 2021 13:45:50: 2000000 INFO @ Sat, 11 Dec 2021 13:45:50: 5000000 INFO @ Sat, 11 Dec 2021 13:45:56: 9000000 INFO @ Sat, 11 Dec 2021 13:45:59: 3000000 INFO @ Sat, 11 Dec 2021 13:45:59: 6000000 INFO @ Sat, 11 Dec 2021 13:46:05: 10000000 INFO @ Sat, 11 Dec 2021 13:46:07: 4000000 INFO @ Sat, 11 Dec 2021 13:46:09: 7000000 INFO @ Sat, 11 Dec 2021 13:46:15: 11000000 INFO @ Sat, 11 Dec 2021 13:46:16: 5000000 INFO @ Sat, 11 Dec 2021 13:46:19: 8000000 INFO @ Sat, 11 Dec 2021 13:46:25: 12000000 INFO @ Sat, 11 Dec 2021 13:46:25: 6000000 INFO @ Sat, 11 Dec 2021 13:46:28: 9000000 INFO @ Sat, 11 Dec 2021 13:46:34: 7000000 INFO @ Sat, 11 Dec 2021 13:46:35: 13000000 INFO @ Sat, 11 Dec 2021 13:46:38: 10000000 INFO @ Sat, 11 Dec 2021 13:46:43: 8000000 INFO @ Sat, 11 Dec 2021 13:46:45: 14000000 INFO @ Sat, 11 Dec 2021 13:46:47: 11000000 INFO @ Sat, 11 Dec 2021 13:46:51: 9000000 INFO @ Sat, 11 Dec 2021 13:46:55: 15000000 INFO @ Sat, 11 Dec 2021 13:46:56: 12000000 INFO @ Sat, 11 Dec 2021 13:47:00: 10000000 INFO @ Sat, 11 Dec 2021 13:47:05: 16000000 INFO @ Sat, 11 Dec 2021 13:47:06: 13000000 INFO @ Sat, 11 Dec 2021 13:47:09: 11000000 INFO @ Sat, 11 Dec 2021 13:47:15: 17000000 INFO @ Sat, 11 Dec 2021 13:47:15: 14000000 INFO @ Sat, 11 Dec 2021 13:47:18: 12000000 INFO @ Sat, 11 Dec 2021 13:47:25: 18000000 INFO @ Sat, 11 Dec 2021 13:47:25: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:47:27: 13000000 INFO @ Sat, 11 Dec 2021 13:47:35: 16000000 INFO @ Sat, 11 Dec 2021 13:47:35: 19000000 INFO @ Sat, 11 Dec 2021 13:47:35: 14000000 INFO @ Sat, 11 Dec 2021 13:47:44: 15000000 INFO @ Sat, 11 Dec 2021 13:47:45: 17000000 INFO @ Sat, 11 Dec 2021 13:47:45: 20000000 INFO @ Sat, 11 Dec 2021 13:47:53: 16000000 INFO @ Sat, 11 Dec 2021 13:47:55: 18000000 INFO @ Sat, 11 Dec 2021 13:47:55: 21000000 INFO @ Sat, 11 Dec 2021 13:48:02: 17000000 INFO @ Sat, 11 Dec 2021 13:48:05: 19000000 INFO @ Sat, 11 Dec 2021 13:48:05: 22000000 INFO @ Sat, 11 Dec 2021 13:48:11: 18000000 INFO @ Sat, 11 Dec 2021 13:48:15: 23000000 INFO @ Sat, 11 Dec 2021 13:48:15: 20000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:48:19: 19000000 INFO @ Sat, 11 Dec 2021 13:48:20: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 13:48:20: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 13:48:20: #1 total tags in treatment: 10527835 INFO @ Sat, 11 Dec 2021 13:48:20: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:48:20: #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 13:48:20: #1 tags after filtering in treatment: 10125045 INFO @ Sat, 11 Dec 2021 13:48:20: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 13:48:20: #1 finished! INFO @ Sat, 11 Dec 2021 13:48:20: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:48:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:48:21: #2 number of paired peaks: 227 WARNING @ Sat, 11 Dec 2021 13:48:21: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Sat, 11 Dec 2021 13:48:21: start model_add_line... INFO @ Sat, 11 Dec 2021 13:48:21: start X-correlation... INFO @ Sat, 11 Dec 2021 13:48:21: end of X-cor INFO @ Sat, 11 Dec 2021 13:48:21: #2 finished! INFO @ Sat, 11 Dec 2021 13:48:21: #2 predicted fragment length is 214 bps INFO @ Sat, 11 Dec 2021 13:48:21: #2 alternative fragment length(s) may be 4,214 bps INFO @ Sat, 11 Dec 2021 13:48:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9008840/SRX9008840.05_model.r INFO @ Sat, 11 Dec 2021 13:48:21: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:48:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:48:24: 21000000 INFO @ Sat, 11 Dec 2021 13:48:28: 20000000 INFO @ Sat, 11 Dec 2021 13:48:34: 22000000 INFO @ Sat, 11 Dec 2021 13:48:37: 21000000 INFO @ Sat, 11 Dec 2021 13:48:42: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:48:44: 23000000 INFO @ Sat, 11 Dec 2021 13:48:45: 22000000 INFO @ Sat, 11 Dec 2021 13:48:49: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 13:48:49: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 13:48:49: #1 total tags in treatment: 10527835 INFO @ Sat, 11 Dec 2021 13:48:49: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:48:49: #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 13:48:49: #1 tags after filtering in treatment: 10125045 INFO @ Sat, 11 Dec 2021 13:48:49: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 13:48:49: #1 finished! INFO @ Sat, 11 Dec 2021 13:48:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:48:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:48:50: #2 number of paired peaks: 227 WARNING @ Sat, 11 Dec 2021 13:48:50: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Sat, 11 Dec 2021 13:48:50: start model_add_line... INFO @ Sat, 11 Dec 2021 13:48:50: start X-correlation... INFO @ Sat, 11 Dec 2021 13:48:50: end of X-cor INFO @ Sat, 11 Dec 2021 13:48:50: #2 finished! INFO @ Sat, 11 Dec 2021 13:48:50: #2 predicted fragment length is 214 bps INFO @ Sat, 11 Dec 2021 13:48:50: #2 alternative fragment length(s) may be 4,214 bps INFO @ Sat, 11 Dec 2021 13:48:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9008840/SRX9008840.10_model.r INFO @ Sat, 11 Dec 2021 13:48:50: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:48:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:48:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9008840/SRX9008840.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:48:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9008840/SRX9008840.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:48:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9008840/SRX9008840.05_summits.bed INFO @ Sat, 11 Dec 2021 13:48:52: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2180 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:48:53: 23000000 INFO @ Sat, 11 Dec 2021 13:48:57: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 13:48:57: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 13:48:57: #1 total tags in treatment: 10527835 INFO @ Sat, 11 Dec 2021 13:48:57: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:48:57: #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 13:48:57: #1 tags after filtering in treatment: 10125045 INFO @ Sat, 11 Dec 2021 13:48:57: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 13:48:57: #1 finished! INFO @ Sat, 11 Dec 2021 13:48:57: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:48:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:48:58: #2 number of paired peaks: 227 WARNING @ Sat, 11 Dec 2021 13:48:58: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Sat, 11 Dec 2021 13:48:58: start model_add_line... INFO @ Sat, 11 Dec 2021 13:48:58: start X-correlation... INFO @ Sat, 11 Dec 2021 13:48:58: end of X-cor INFO @ Sat, 11 Dec 2021 13:48:58: #2 finished! INFO @ Sat, 11 Dec 2021 13:48:58: #2 predicted fragment length is 214 bps INFO @ Sat, 11 Dec 2021 13:48:58: #2 alternative fragment length(s) may be 4,214 bps INFO @ Sat, 11 Dec 2021 13:48:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9008840/SRX9008840.20_model.r INFO @ Sat, 11 Dec 2021 13:48:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:48:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:49:11: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:49:18: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:49:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9008840/SRX9008840.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:49:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9008840/SRX9008840.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:49:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9008840/SRX9008840.10_summits.bed INFO @ Sat, 11 Dec 2021 13:49:21: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (846 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:49:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9008840/SRX9008840.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:49:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9008840/SRX9008840.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:49:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9008840/SRX9008840.20_summits.bed INFO @ Sat, 11 Dec 2021 13:49:28: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (313 records, 4 fields): 2 millis CompletedMACS2peakCalling