Job ID = 14167231 SRX = SRX8973514 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21802032 spots for SRR12901794/SRR12901794.sra Written 21802032 spots for SRR12901794/SRR12901794.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167904 ("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: 00:27:39 21802032 reads; of these: 21802032 (100.00%) were paired; of these: 9028999 (41.41%) aligned concordantly 0 times 8973163 (41.16%) aligned concordantly exactly 1 time 3799870 (17.43%) aligned concordantly >1 times ---- 9028999 pairs aligned concordantly 0 times; of these: 188950 (2.09%) aligned discordantly 1 time ---- 8840049 pairs aligned 0 times concordantly or discordantly; of these: 17680098 mates make up the pairs; of these: 16459753 (93.10%) aligned 0 times 750918 (4.25%) aligned exactly 1 time 469427 (2.66%) aligned >1 times 62.25% overall alignment rate Time searching: 00:27:40 Overall time: 00:27:40 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] 632453 / 12951033 = 0.0488 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 11:44:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8973514/SRX8973514.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8973514/SRX8973514.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8973514/SRX8973514.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8973514/SRX8973514.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 11:44:03: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:44:03: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:44:07: 1000000 INFO @ Fri, 10 Dec 2021 11:44:11: 2000000 INFO @ Fri, 10 Dec 2021 11:44:15: 3000000 INFO @ Fri, 10 Dec 2021 11:44:19: 4000000 INFO @ Fri, 10 Dec 2021 11:44:23: 5000000 INFO @ Fri, 10 Dec 2021 11:44:27: 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 @ Fri, 10 Dec 2021 11:44:32: 7000000 INFO @ Fri, 10 Dec 2021 11:44:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8973514/SRX8973514.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8973514/SRX8973514.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8973514/SRX8973514.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8973514/SRX8973514.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 11:44:33: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:44:33: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:44:36: 8000000 INFO @ Fri, 10 Dec 2021 11:44:38: 1000000 INFO @ Fri, 10 Dec 2021 11:44:40: 9000000 INFO @ Fri, 10 Dec 2021 11:44:43: 2000000 INFO @ Fri, 10 Dec 2021 11:44:44: 10000000 INFO @ Fri, 10 Dec 2021 11:44:48: 11000000 INFO @ Fri, 10 Dec 2021 11:44:48: 3000000 INFO @ Fri, 10 Dec 2021 11:44:53: 12000000 INFO @ Fri, 10 Dec 2021 11:44:53: 4000000 INFO @ Fri, 10 Dec 2021 11:44:57: 13000000 INFO @ Fri, 10 Dec 2021 11:44:59: 5000000 INFO @ Fri, 10 Dec 2021 11:45:01: 14000000 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 11:45:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8973514/SRX8973514.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8973514/SRX8973514.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8973514/SRX8973514.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8973514/SRX8973514.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 11:45:03: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:45:03: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:45:04: 6000000 INFO @ Fri, 10 Dec 2021 11:45:05: 15000000 INFO @ Fri, 10 Dec 2021 11:45:07: 1000000 INFO @ Fri, 10 Dec 2021 11:45:09: 7000000 INFO @ Fri, 10 Dec 2021 11:45:09: 16000000 INFO @ Fri, 10 Dec 2021 11:45:11: 2000000 INFO @ Fri, 10 Dec 2021 11:45:14: 17000000 INFO @ Fri, 10 Dec 2021 11:45:14: 8000000 INFO @ Fri, 10 Dec 2021 11:45:16: 3000000 INFO @ Fri, 10 Dec 2021 11:45:18: 18000000 INFO @ Fri, 10 Dec 2021 11:45:19: 9000000 INFO @ Fri, 10 Dec 2021 11:45:20: 4000000 INFO @ Fri, 10 Dec 2021 11:45:22: 19000000 INFO @ Fri, 10 Dec 2021 11:45:24: 5000000 INFO @ Fri, 10 Dec 2021 11:45:24: 10000000 INFO @ Fri, 10 Dec 2021 11:45:26: 20000000 INFO @ Fri, 10 Dec 2021 11:45:28: 6000000 INFO @ Fri, 10 Dec 2021 11:45:29: 11000000 INFO @ Fri, 10 Dec 2021 11:45:31: 21000000 INFO @ Fri, 10 Dec 2021 11:45:32: 7000000 INFO @ Fri, 10 Dec 2021 11:45:34: 12000000 INFO @ Fri, 10 Dec 2021 11:45:35: 22000000 INFO @ Fri, 10 Dec 2021 11:45:37: 8000000 INFO @ Fri, 10 Dec 2021 11:45:39: 23000000 INFO @ Fri, 10 Dec 2021 11:45:40: 13000000 INFO @ Fri, 10 Dec 2021 11:45:41: 9000000 INFO @ Fri, 10 Dec 2021 11:45:43: 24000000 INFO @ Fri, 10 Dec 2021 11:45:45: 14000000 INFO @ Fri, 10 Dec 2021 11:45:45: 10000000 INFO @ Fri, 10 Dec 2021 11:45:47: 25000000 INFO @ Fri, 10 Dec 2021 11:45:49: 11000000 INFO @ Fri, 10 Dec 2021 11:45:50: 15000000 INFO @ Fri, 10 Dec 2021 11:45:51: #1 tag size is determined as 42 bps INFO @ Fri, 10 Dec 2021 11:45:51: #1 tag size = 42 INFO @ Fri, 10 Dec 2021 11:45:51: #1 total tags in treatment: 12143891 INFO @ Fri, 10 Dec 2021 11:45:51: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:45:51: #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 11:45:51: #1 tags after filtering in treatment: 11602093 INFO @ Fri, 10 Dec 2021 11:45:51: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 10 Dec 2021 11:45:51: #1 finished! INFO @ Fri, 10 Dec 2021 11:45:51: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:45:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:45:52: #2 number of paired peaks: 171 WARNING @ Fri, 10 Dec 2021 11:45:52: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Fri, 10 Dec 2021 11:45:52: start model_add_line... INFO @ Fri, 10 Dec 2021 11:45:52: start X-correlation... INFO @ Fri, 10 Dec 2021 11:45:52: end of X-cor INFO @ Fri, 10 Dec 2021 11:45:52: #2 finished! INFO @ Fri, 10 Dec 2021 11:45:52: #2 predicted fragment length is 167 bps INFO @ Fri, 10 Dec 2021 11:45:52: #2 alternative fragment length(s) may be 167 bps INFO @ Fri, 10 Dec 2021 11:45:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8973514/SRX8973514.05_model.r INFO @ Fri, 10 Dec 2021 11:45:52: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:45:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:45:53: 12000000 INFO @ Fri, 10 Dec 2021 11:45:55: 16000000 INFO @ Fri, 10 Dec 2021 11:45:58: 13000000 INFO @ Fri, 10 Dec 2021 11:46:00: 17000000 INFO @ Fri, 10 Dec 2021 11:46:02: 14000000 INFO @ Fri, 10 Dec 2021 11:46:05: 18000000 INFO @ Fri, 10 Dec 2021 11:46:06: 15000000 INFO @ Fri, 10 Dec 2021 11:46:10: 16000000 INFO @ Fri, 10 Dec 2021 11:46:10: 19000000 INFO @ Fri, 10 Dec 2021 11:46:14: 17000000 INFO @ Fri, 10 Dec 2021 11:46:14: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:46:15: 20000000 INFO @ Fri, 10 Dec 2021 11:46:18: 18000000 INFO @ Fri, 10 Dec 2021 11:46:21: 21000000 INFO @ Fri, 10 Dec 2021 11:46:23: 19000000 INFO @ Fri, 10 Dec 2021 11:46:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8973514/SRX8973514.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:46:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8973514/SRX8973514.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:46:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8973514/SRX8973514.05_summits.bed INFO @ Fri, 10 Dec 2021 11:46:25: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1240 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:46:26: 22000000 INFO @ Fri, 10 Dec 2021 11:46:27: 20000000 INFO @ Fri, 10 Dec 2021 11:46:31: 23000000 INFO @ Fri, 10 Dec 2021 11:46:31: 21000000 INFO @ Fri, 10 Dec 2021 11:46:35: 22000000 INFO @ Fri, 10 Dec 2021 11:46:36: 24000000 INFO @ Fri, 10 Dec 2021 11:46:39: 23000000 INFO @ Fri, 10 Dec 2021 11:46:41: 25000000 INFO @ Fri, 10 Dec 2021 11:46:44: 24000000 INFO @ Fri, 10 Dec 2021 11:46:46: #1 tag size is determined as 42 bps INFO @ Fri, 10 Dec 2021 11:46:46: #1 tag size = 42 INFO @ Fri, 10 Dec 2021 11:46:46: #1 total tags in treatment: 12143891 INFO @ Fri, 10 Dec 2021 11:46:46: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:46:46: #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 11:46:46: #1 tags after filtering in treatment: 11602093 INFO @ Fri, 10 Dec 2021 11:46:46: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 10 Dec 2021 11:46:46: #1 finished! INFO @ Fri, 10 Dec 2021 11:46:46: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:46:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:46:47: #2 number of paired peaks: 171 WARNING @ Fri, 10 Dec 2021 11:46:47: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Fri, 10 Dec 2021 11:46:47: start model_add_line... INFO @ Fri, 10 Dec 2021 11:46:47: start X-correlation... INFO @ Fri, 10 Dec 2021 11:46:47: end of X-cor INFO @ Fri, 10 Dec 2021 11:46:47: #2 finished! INFO @ Fri, 10 Dec 2021 11:46:47: #2 predicted fragment length is 167 bps INFO @ Fri, 10 Dec 2021 11:46:47: #2 alternative fragment length(s) may be 167 bps INFO @ Fri, 10 Dec 2021 11:46:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8973514/SRX8973514.10_model.r INFO @ Fri, 10 Dec 2021 11:46:47: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:46:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:46:48: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:46:51: #1 tag size is determined as 42 bps INFO @ Fri, 10 Dec 2021 11:46:51: #1 tag size = 42 INFO @ Fri, 10 Dec 2021 11:46:51: #1 total tags in treatment: 12143891 INFO @ Fri, 10 Dec 2021 11:46:51: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:46:51: #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 11:46:52: #1 tags after filtering in treatment: 11602093 INFO @ Fri, 10 Dec 2021 11:46:52: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 10 Dec 2021 11:46:52: #1 finished! INFO @ Fri, 10 Dec 2021 11:46:52: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:46:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:46:52: #2 number of paired peaks: 171 WARNING @ Fri, 10 Dec 2021 11:46:52: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Fri, 10 Dec 2021 11:46:52: start model_add_line... INFO @ Fri, 10 Dec 2021 11:46:52: start X-correlation... INFO @ Fri, 10 Dec 2021 11:46:52: end of X-cor INFO @ Fri, 10 Dec 2021 11:46:52: #2 finished! INFO @ Fri, 10 Dec 2021 11:46:52: #2 predicted fragment length is 167 bps INFO @ Fri, 10 Dec 2021 11:46:52: #2 alternative fragment length(s) may be 167 bps INFO @ Fri, 10 Dec 2021 11:46:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8973514/SRX8973514.20_model.r INFO @ Fri, 10 Dec 2021 11:46:52: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:46:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:47:09: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:47:15: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:47:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8973514/SRX8973514.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:47:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8973514/SRX8973514.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:47:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8973514/SRX8973514.10_summits.bed INFO @ Fri, 10 Dec 2021 11:47:20: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (757 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:47:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8973514/SRX8973514.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:47:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8973514/SRX8973514.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:47:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8973514/SRX8973514.20_summits.bed INFO @ Fri, 10 Dec 2021 11:47:26: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (524 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。