Job ID = 14171798 SRX = SRX10386241 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 22197320 spots for SRR14009306/SRR14009306.sra Written 22197320 spots for SRR14009306/SRR14009306.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172427 ("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: 00:42:06 22197320 reads; of these: 22197320 (100.00%) were paired; of these: 1887994 (8.51%) aligned concordantly 0 times 13667806 (61.57%) aligned concordantly exactly 1 time 6641520 (29.92%) aligned concordantly >1 times ---- 1887994 pairs aligned concordantly 0 times; of these: 138567 (7.34%) aligned discordantly 1 time ---- 1749427 pairs aligned 0 times concordantly or discordantly; of these: 3498854 mates make up the pairs; of these: 2692195 (76.95%) aligned 0 times 463195 (13.24%) aligned exactly 1 time 343464 (9.82%) aligned >1 times 93.94% overall alignment rate Time searching: 00:42:06 Overall time: 00:42:06 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 20 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] 1564319 / 20413776 = 0.0766 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 13:46:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386241/SRX10386241.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386241/SRX10386241.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386241/SRX10386241.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386241/SRX10386241.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 13:46:17: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:46:17: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:46:22: 1000000 INFO @ Sat, 11 Dec 2021 13:46:26: 2000000 INFO @ Sat, 11 Dec 2021 13:46:30: 3000000 INFO @ Sat, 11 Dec 2021 13:46:34: 4000000 INFO @ Sat, 11 Dec 2021 13:46:38: 5000000 INFO @ Sat, 11 Dec 2021 13:46:42: 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 13:46:46: 7000000 INFO @ Sat, 11 Dec 2021 13:46:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386241/SRX10386241.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386241/SRX10386241.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386241/SRX10386241.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386241/SRX10386241.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 13:46:47: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:46:47: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:46:50: 8000000 INFO @ Sat, 11 Dec 2021 13:46:52: 1000000 INFO @ Sat, 11 Dec 2021 13:46:54: 9000000 INFO @ Sat, 11 Dec 2021 13:46:56: 2000000 INFO @ Sat, 11 Dec 2021 13:46:59: 10000000 INFO @ Sat, 11 Dec 2021 13:47:00: 3000000 INFO @ Sat, 11 Dec 2021 13:47:03: 11000000 INFO @ Sat, 11 Dec 2021 13:47:04: 4000000 INFO @ Sat, 11 Dec 2021 13:47:07: 12000000 INFO @ Sat, 11 Dec 2021 13:47:08: 5000000 INFO @ Sat, 11 Dec 2021 13:47:11: 13000000 INFO @ Sat, 11 Dec 2021 13:47:12: 6000000 INFO @ Sat, 11 Dec 2021 13:47:15: 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 @ Sat, 11 Dec 2021 13:47:16: 7000000 INFO @ Sat, 11 Dec 2021 13:47:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386241/SRX10386241.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386241/SRX10386241.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386241/SRX10386241.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386241/SRX10386241.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 13:47:17: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:47:17: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:47:19: 15000000 INFO @ Sat, 11 Dec 2021 13:47:21: 8000000 INFO @ Sat, 11 Dec 2021 13:47:22: 1000000 INFO @ Sat, 11 Dec 2021 13:47:23: 16000000 INFO @ Sat, 11 Dec 2021 13:47:25: 9000000 INFO @ Sat, 11 Dec 2021 13:47:26: 2000000 INFO @ Sat, 11 Dec 2021 13:47:28: 17000000 INFO @ Sat, 11 Dec 2021 13:47:29: 10000000 INFO @ Sat, 11 Dec 2021 13:47:30: 3000000 INFO @ Sat, 11 Dec 2021 13:47:32: 18000000 INFO @ Sat, 11 Dec 2021 13:47:33: 11000000 INFO @ Sat, 11 Dec 2021 13:47:34: 4000000 INFO @ Sat, 11 Dec 2021 13:47:36: 19000000 INFO @ Sat, 11 Dec 2021 13:47:37: 12000000 INFO @ Sat, 11 Dec 2021 13:47:38: 5000000 INFO @ Sat, 11 Dec 2021 13:47:40: 20000000 INFO @ Sat, 11 Dec 2021 13:47:41: 13000000 INFO @ Sat, 11 Dec 2021 13:47:42: 6000000 INFO @ Sat, 11 Dec 2021 13:47:44: 21000000 INFO @ Sat, 11 Dec 2021 13:47:46: 14000000 INFO @ Sat, 11 Dec 2021 13:47:47: 7000000 INFO @ Sat, 11 Dec 2021 13:47:48: 22000000 INFO @ Sat, 11 Dec 2021 13:47:50: 15000000 INFO @ Sat, 11 Dec 2021 13:47:51: 8000000 INFO @ Sat, 11 Dec 2021 13:47:52: 23000000 INFO @ Sat, 11 Dec 2021 13:47:54: 16000000 INFO @ Sat, 11 Dec 2021 13:47:55: 9000000 INFO @ Sat, 11 Dec 2021 13:47:57: 24000000 INFO @ Sat, 11 Dec 2021 13:47:58: 17000000 INFO @ Sat, 11 Dec 2021 13:47:59: 10000000 INFO @ Sat, 11 Dec 2021 13:48:01: 25000000 INFO @ Sat, 11 Dec 2021 13:48:02: 18000000 INFO @ Sat, 11 Dec 2021 13:48:03: 11000000 INFO @ Sat, 11 Dec 2021 13:48:05: 26000000 INFO @ Sat, 11 Dec 2021 13:48:06: 19000000 INFO @ Sat, 11 Dec 2021 13:48:07: 12000000 INFO @ Sat, 11 Dec 2021 13:48:09: 27000000 INFO @ Sat, 11 Dec 2021 13:48:10: 20000000 INFO @ Sat, 11 Dec 2021 13:48:12: 13000000 INFO @ Sat, 11 Dec 2021 13:48:13: 28000000 INFO @ Sat, 11 Dec 2021 13:48:15: 21000000 INFO @ Sat, 11 Dec 2021 13:48:16: 14000000 INFO @ Sat, 11 Dec 2021 13:48:17: 29000000 INFO @ Sat, 11 Dec 2021 13:48:19: 22000000 INFO @ Sat, 11 Dec 2021 13:48:20: 15000000 INFO @ Sat, 11 Dec 2021 13:48:22: 30000000 INFO @ Sat, 11 Dec 2021 13:48:23: 23000000 INFO @ Sat, 11 Dec 2021 13:48:24: 16000000 INFO @ Sat, 11 Dec 2021 13:48:26: 31000000 INFO @ Sat, 11 Dec 2021 13:48:27: 24000000 INFO @ Sat, 11 Dec 2021 13:48:28: 17000000 INFO @ Sat, 11 Dec 2021 13:48:30: 32000000 INFO @ Sat, 11 Dec 2021 13:48:31: 25000000 INFO @ Sat, 11 Dec 2021 13:48:32: 18000000 INFO @ Sat, 11 Dec 2021 13:48:34: 33000000 INFO @ Sat, 11 Dec 2021 13:48:35: 26000000 INFO @ Sat, 11 Dec 2021 13:48:37: 19000000 INFO @ Sat, 11 Dec 2021 13:48:38: 34000000 INFO @ Sat, 11 Dec 2021 13:48:40: 27000000 INFO @ Sat, 11 Dec 2021 13:48:41: 20000000 INFO @ Sat, 11 Dec 2021 13:48:43: 35000000 INFO @ Sat, 11 Dec 2021 13:48:44: 28000000 INFO @ Sat, 11 Dec 2021 13:48:45: 21000000 INFO @ Sat, 11 Dec 2021 13:48:47: 36000000 INFO @ Sat, 11 Dec 2021 13:48:48: 29000000 INFO @ Sat, 11 Dec 2021 13:48:49: 22000000 INFO @ Sat, 11 Dec 2021 13:48:51: 37000000 INFO @ Sat, 11 Dec 2021 13:48:52: 30000000 INFO @ Sat, 11 Dec 2021 13:48:53: 23000000 INFO @ Sat, 11 Dec 2021 13:48:55: 38000000 INFO @ Sat, 11 Dec 2021 13:48:56: 31000000 INFO @ Sat, 11 Dec 2021 13:48:57: 24000000 INFO @ Sat, 11 Dec 2021 13:48:58: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:48:58: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:48:58: #1 total tags in treatment: 18745808 INFO @ Sat, 11 Dec 2021 13:48:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:48:58: #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 13:48:58: #1 tags after filtering in treatment: 15518026 INFO @ Sat, 11 Dec 2021 13:48:58: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 11 Dec 2021 13:48:58: #1 finished! INFO @ Sat, 11 Dec 2021 13:48:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:48:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:48:59: #2 number of paired peaks: 115 WARNING @ Sat, 11 Dec 2021 13:48:59: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Sat, 11 Dec 2021 13:48:59: start model_add_line... INFO @ Sat, 11 Dec 2021 13:48:59: start X-correlation... INFO @ Sat, 11 Dec 2021 13:48:59: end of X-cor INFO @ Sat, 11 Dec 2021 13:48:59: #2 finished! INFO @ Sat, 11 Dec 2021 13:48:59: #2 predicted fragment length is 111 bps INFO @ Sat, 11 Dec 2021 13:48:59: #2 alternative fragment length(s) may be 111 bps INFO @ Sat, 11 Dec 2021 13:48:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386241/SRX10386241.05_model.r INFO @ Sat, 11 Dec 2021 13:48:59: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:48:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:49:00: 32000000 INFO @ Sat, 11 Dec 2021 13:49:02: 25000000 INFO @ Sat, 11 Dec 2021 13:49:05: 33000000 INFO @ Sat, 11 Dec 2021 13:49:06: 26000000 INFO @ Sat, 11 Dec 2021 13:49:09: 34000000 INFO @ Sat, 11 Dec 2021 13:49:10: 27000000 INFO @ Sat, 11 Dec 2021 13:49:13: 35000000 INFO @ Sat, 11 Dec 2021 13:49:14: 28000000 INFO @ Sat, 11 Dec 2021 13:49:17: 36000000 INFO @ Sat, 11 Dec 2021 13:49:18: 29000000 INFO @ Sat, 11 Dec 2021 13:49:21: 37000000 INFO @ Sat, 11 Dec 2021 13:49:22: 30000000 INFO @ Sat, 11 Dec 2021 13:49:25: 38000000 INFO @ Sat, 11 Dec 2021 13:49:26: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:49:27: 31000000 INFO @ Sat, 11 Dec 2021 13:49:28: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:49:28: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:49:28: #1 total tags in treatment: 18745808 INFO @ Sat, 11 Dec 2021 13:49:28: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:49:28: #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 13:49:28: #1 tags after filtering in treatment: 15518026 INFO @ Sat, 11 Dec 2021 13:49:28: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 11 Dec 2021 13:49:28: #1 finished! INFO @ Sat, 11 Dec 2021 13:49:28: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:49:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:49:29: #2 number of paired peaks: 115 WARNING @ Sat, 11 Dec 2021 13:49:29: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Sat, 11 Dec 2021 13:49:29: start model_add_line... INFO @ Sat, 11 Dec 2021 13:49:29: start X-correlation... INFO @ Sat, 11 Dec 2021 13:49:29: end of X-cor INFO @ Sat, 11 Dec 2021 13:49:29: #2 finished! INFO @ Sat, 11 Dec 2021 13:49:29: #2 predicted fragment length is 111 bps INFO @ Sat, 11 Dec 2021 13:49:29: #2 alternative fragment length(s) may be 111 bps INFO @ Sat, 11 Dec 2021 13:49:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386241/SRX10386241.10_model.r INFO @ Sat, 11 Dec 2021 13:49:29: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:49:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:49:31: 32000000 INFO @ Sat, 11 Dec 2021 13:49:35: 33000000 INFO @ Sat, 11 Dec 2021 13:49:39: 34000000 INFO @ Sat, 11 Dec 2021 13:49:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386241/SRX10386241.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:49:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386241/SRX10386241.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:49:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386241/SRX10386241.05_summits.bed INFO @ Sat, 11 Dec 2021 13:49:41: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1416 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:49:43: 35000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:49:47: 36000000 INFO @ Sat, 11 Dec 2021 13:49:51: 37000000 INFO @ Sat, 11 Dec 2021 13:49:56: 38000000 INFO @ Sat, 11 Dec 2021 13:49:57: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:49:58: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:49:58: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:49:58: #1 total tags in treatment: 18745808 INFO @ Sat, 11 Dec 2021 13:49:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:49:58: #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 13:49:58: #1 tags after filtering in treatment: 15518026 INFO @ Sat, 11 Dec 2021 13:49:58: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 11 Dec 2021 13:49:58: #1 finished! INFO @ Sat, 11 Dec 2021 13:49:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:49:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:49:59: #2 number of paired peaks: 115 WARNING @ Sat, 11 Dec 2021 13:49:59: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Sat, 11 Dec 2021 13:49:59: start model_add_line... INFO @ Sat, 11 Dec 2021 13:49:59: start X-correlation... INFO @ Sat, 11 Dec 2021 13:49:59: end of X-cor INFO @ Sat, 11 Dec 2021 13:49:59: #2 finished! INFO @ Sat, 11 Dec 2021 13:49:59: #2 predicted fragment length is 111 bps INFO @ Sat, 11 Dec 2021 13:49:59: #2 alternative fragment length(s) may be 111 bps INFO @ Sat, 11 Dec 2021 13:49:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386241/SRX10386241.20_model.r INFO @ Sat, 11 Dec 2021 13:49:59: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:49:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:50:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386241/SRX10386241.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:50:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386241/SRX10386241.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:50:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386241/SRX10386241.10_summits.bed INFO @ Sat, 11 Dec 2021 13:50:11: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (960 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:50:27: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:50:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386241/SRX10386241.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:50:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386241/SRX10386241.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:50:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386241/SRX10386241.20_summits.bed INFO @ Sat, 11 Dec 2021 13:50:41: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (634 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。