Job ID = 14171659 SRX = SRX10386217 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 22326542 spots for SRR14009282/SRR14009282.sra Written 22326542 spots for SRR14009282/SRR14009282.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172307 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:55:53 22326542 reads; of these: 22326542 (100.00%) were paired; of these: 4001751 (17.92%) aligned concordantly 0 times 12936841 (57.94%) aligned concordantly exactly 1 time 5387950 (24.13%) aligned concordantly >1 times ---- 4001751 pairs aligned concordantly 0 times; of these: 763548 (19.08%) aligned discordantly 1 time ---- 3238203 pairs aligned 0 times concordantly or discordantly; of these: 6476406 mates make up the pairs; of these: 5063000 (78.18%) aligned 0 times 634810 (9.80%) aligned exactly 1 time 778596 (12.02%) aligned >1 times 88.66% overall alignment rate Time searching: 00:55:54 Overall time: 00:55:54 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] 1836261 / 19052525 = 0.0964 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 13:28:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386217/SRX10386217.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386217/SRX10386217.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386217/SRX10386217.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386217/SRX10386217.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 13:28:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:28:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:28:39: 1000000 INFO @ Sat, 11 Dec 2021 13:28:45: 2000000 INFO @ Sat, 11 Dec 2021 13:28:52: 3000000 INFO @ Sat, 11 Dec 2021 13:28:58: 4000000 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 13:29:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386217/SRX10386217.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386217/SRX10386217.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386217/SRX10386217.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386217/SRX10386217.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 13:29:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:29:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:29:04: 5000000 INFO @ Sat, 11 Dec 2021 13:29:09: 1000000 INFO @ Sat, 11 Dec 2021 13:29:11: 6000000 INFO @ Sat, 11 Dec 2021 13:29:17: 2000000 INFO @ Sat, 11 Dec 2021 13:29:18: 7000000 INFO @ Sat, 11 Dec 2021 13:29:24: 8000000 INFO @ Sat, 11 Dec 2021 13:29:25: 3000000 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 13:29:30: 9000000 INFO @ Sat, 11 Dec 2021 13:29:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386217/SRX10386217.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386217/SRX10386217.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386217/SRX10386217.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386217/SRX10386217.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 13:29:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:29:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:29:33: 4000000 INFO @ Sat, 11 Dec 2021 13:29:38: 10000000 INFO @ Sat, 11 Dec 2021 13:29:39: 1000000 INFO @ Sat, 11 Dec 2021 13:29:41: 5000000 INFO @ Sat, 11 Dec 2021 13:29:45: 11000000 INFO @ Sat, 11 Dec 2021 13:29:46: 2000000 INFO @ Sat, 11 Dec 2021 13:29:49: 6000000 INFO @ Sat, 11 Dec 2021 13:29:52: 12000000 INFO @ Sat, 11 Dec 2021 13:29:54: 3000000 INFO @ Sat, 11 Dec 2021 13:29:57: 7000000 INFO @ Sat, 11 Dec 2021 13:29:59: 13000000 INFO @ Sat, 11 Dec 2021 13:30:01: 4000000 INFO @ Sat, 11 Dec 2021 13:30:05: 8000000 INFO @ Sat, 11 Dec 2021 13:30:06: 14000000 INFO @ Sat, 11 Dec 2021 13:30:08: 5000000 INFO @ Sat, 11 Dec 2021 13:30:13: 9000000 INFO @ Sat, 11 Dec 2021 13:30:14: 15000000 INFO @ Sat, 11 Dec 2021 13:30:16: 6000000 INFO @ Sat, 11 Dec 2021 13:30:21: 10000000 INFO @ Sat, 11 Dec 2021 13:30:21: 16000000 INFO @ Sat, 11 Dec 2021 13:30:23: 7000000 INFO @ Sat, 11 Dec 2021 13:30:28: 17000000 INFO @ Sat, 11 Dec 2021 13:30:29: 11000000 INFO @ Sat, 11 Dec 2021 13:30:30: 8000000 INFO @ Sat, 11 Dec 2021 13:30:35: 18000000 INFO @ Sat, 11 Dec 2021 13:30:37: 12000000 INFO @ Sat, 11 Dec 2021 13:30:37: 9000000 INFO @ Sat, 11 Dec 2021 13:30:42: 19000000 INFO @ Sat, 11 Dec 2021 13:30:45: 10000000 INFO @ Sat, 11 Dec 2021 13:30:45: 13000000 INFO @ Sat, 11 Dec 2021 13:30:50: 20000000 INFO @ Sat, 11 Dec 2021 13:30:52: 11000000 INFO @ Sat, 11 Dec 2021 13:30:53: 14000000 INFO @ Sat, 11 Dec 2021 13:30:57: 21000000 INFO @ Sat, 11 Dec 2021 13:30:59: 12000000 INFO @ Sat, 11 Dec 2021 13:31:02: 15000000 INFO @ Sat, 11 Dec 2021 13:31:04: 22000000 INFO @ Sat, 11 Dec 2021 13:31:06: 13000000 INFO @ Sat, 11 Dec 2021 13:31:10: 16000000 INFO @ Sat, 11 Dec 2021 13:31:11: 23000000 INFO @ Sat, 11 Dec 2021 13:31:13: 14000000 INFO @ Sat, 11 Dec 2021 13:31:18: 24000000 INFO @ Sat, 11 Dec 2021 13:31:18: 17000000 INFO @ Sat, 11 Dec 2021 13:31:21: 15000000 INFO @ Sat, 11 Dec 2021 13:31:25: 25000000 INFO @ Sat, 11 Dec 2021 13:31:26: 18000000 INFO @ Sat, 11 Dec 2021 13:31:28: 16000000 INFO @ Sat, 11 Dec 2021 13:31:32: 26000000 INFO @ Sat, 11 Dec 2021 13:31:34: 19000000 INFO @ Sat, 11 Dec 2021 13:31:35: 17000000 INFO @ Sat, 11 Dec 2021 13:31:40: 27000000 INFO @ Sat, 11 Dec 2021 13:31:42: 20000000 INFO @ Sat, 11 Dec 2021 13:31:42: 18000000 INFO @ Sat, 11 Dec 2021 13:31:47: 28000000 INFO @ Sat, 11 Dec 2021 13:31:49: 19000000 INFO @ Sat, 11 Dec 2021 13:31:50: 21000000 INFO @ Sat, 11 Dec 2021 13:31:54: 29000000 INFO @ Sat, 11 Dec 2021 13:31:57: 20000000 INFO @ Sat, 11 Dec 2021 13:31:58: 22000000 INFO @ Sat, 11 Dec 2021 13:32:01: 30000000 INFO @ Sat, 11 Dec 2021 13:32:04: 21000000 INFO @ Sat, 11 Dec 2021 13:32:07: 23000000 INFO @ Sat, 11 Dec 2021 13:32:08: 31000000 INFO @ Sat, 11 Dec 2021 13:32:11: 22000000 INFO @ Sat, 11 Dec 2021 13:32:14: 24000000 INFO @ Sat, 11 Dec 2021 13:32:17: 32000000 INFO @ Sat, 11 Dec 2021 13:32:18: 23000000 INFO @ Sat, 11 Dec 2021 13:32:22: 25000000 INFO @ Sat, 11 Dec 2021 13:32:25: 33000000 INFO @ Sat, 11 Dec 2021 13:32:26: 24000000 INFO @ Sat, 11 Dec 2021 13:32:31: 26000000 INFO @ Sat, 11 Dec 2021 13:32:32: 34000000 INFO @ Sat, 11 Dec 2021 13:32:33: 25000000 INFO @ Sat, 11 Dec 2021 13:32:39: 35000000 INFO @ Sat, 11 Dec 2021 13:32:39: 27000000 INFO @ Sat, 11 Dec 2021 13:32:40: 26000000 INFO @ Sat, 11 Dec 2021 13:32:46: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:32:46: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:32:46: #1 total tags in treatment: 16505908 INFO @ Sat, 11 Dec 2021 13:32:46: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:32:46: #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 13:32:46: #1 tags after filtering in treatment: 13465364 INFO @ Sat, 11 Dec 2021 13:32:46: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 11 Dec 2021 13:32:46: #1 finished! INFO @ Sat, 11 Dec 2021 13:32:46: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:32:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:32:47: #2 number of paired peaks: 169 WARNING @ Sat, 11 Dec 2021 13:32:47: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sat, 11 Dec 2021 13:32:47: start model_add_line... INFO @ Sat, 11 Dec 2021 13:32:47: start X-correlation... INFO @ Sat, 11 Dec 2021 13:32:47: end of X-cor INFO @ Sat, 11 Dec 2021 13:32:47: #2 finished! INFO @ Sat, 11 Dec 2021 13:32:47: #2 predicted fragment length is 108 bps INFO @ Sat, 11 Dec 2021 13:32:47: #2 alternative fragment length(s) may be 108 bps INFO @ Sat, 11 Dec 2021 13:32:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386217/SRX10386217.05_model.r INFO @ Sat, 11 Dec 2021 13:32:47: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:32:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:32:47: 27000000 INFO @ Sat, 11 Dec 2021 13:32:48: 28000000 INFO @ Sat, 11 Dec 2021 13:32:54: 28000000 INFO @ Sat, 11 Dec 2021 13:32:56: 29000000 INFO @ Sat, 11 Dec 2021 13:33:01: 29000000 INFO @ Sat, 11 Dec 2021 13:33:04: 30000000 INFO @ Sat, 11 Dec 2021 13:33:07: 30000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:33:12: 31000000 INFO @ Sat, 11 Dec 2021 13:33:12: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:33:14: 31000000 INFO @ Sat, 11 Dec 2021 13:33:20: 32000000 INFO @ Sat, 11 Dec 2021 13:33:21: 32000000 INFO @ Sat, 11 Dec 2021 13:33:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386217/SRX10386217.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:33:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386217/SRX10386217.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:33:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386217/SRX10386217.05_summits.bed INFO @ Sat, 11 Dec 2021 13:33:27: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1758 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:33:28: 33000000 INFO @ Sat, 11 Dec 2021 13:33:28: 33000000 INFO @ Sat, 11 Dec 2021 13:33:35: 34000000 INFO @ Sat, 11 Dec 2021 13:33:36: 34000000 INFO @ Sat, 11 Dec 2021 13:33:42: 35000000 INFO @ Sat, 11 Dec 2021 13:33:44: 35000000 INFO @ Sat, 11 Dec 2021 13:33:48: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:33:48: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:33:48: #1 total tags in treatment: 16505908 INFO @ Sat, 11 Dec 2021 13:33:48: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:33:48: #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 13:33:49: #1 tags after filtering in treatment: 13465364 INFO @ Sat, 11 Dec 2021 13:33:49: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 11 Dec 2021 13:33:49: #1 finished! INFO @ Sat, 11 Dec 2021 13:33:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:33:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:33:49: #2 number of paired peaks: 169 WARNING @ Sat, 11 Dec 2021 13:33:49: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sat, 11 Dec 2021 13:33:49: start model_add_line... INFO @ Sat, 11 Dec 2021 13:33:50: start X-correlation... INFO @ Sat, 11 Dec 2021 13:33:50: end of X-cor INFO @ Sat, 11 Dec 2021 13:33:50: #2 finished! INFO @ Sat, 11 Dec 2021 13:33:50: #2 predicted fragment length is 108 bps INFO @ Sat, 11 Dec 2021 13:33:50: #2 alternative fragment length(s) may be 108 bps INFO @ Sat, 11 Dec 2021 13:33:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386217/SRX10386217.20_model.r INFO @ Sat, 11 Dec 2021 13:33:50: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:33:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:33:51: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:33:51: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:33:51: #1 total tags in treatment: 16505908 INFO @ Sat, 11 Dec 2021 13:33:51: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:33:51: #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 13:33:51: #1 tags after filtering in treatment: 13465364 INFO @ Sat, 11 Dec 2021 13:33:51: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 11 Dec 2021 13:33:51: #1 finished! INFO @ Sat, 11 Dec 2021 13:33:51: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:33:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:33:52: #2 number of paired peaks: 169 WARNING @ Sat, 11 Dec 2021 13:33:52: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sat, 11 Dec 2021 13:33:52: start model_add_line... INFO @ Sat, 11 Dec 2021 13:33:52: start X-correlation... INFO @ Sat, 11 Dec 2021 13:33:52: end of X-cor INFO @ Sat, 11 Dec 2021 13:33:52: #2 finished! INFO @ Sat, 11 Dec 2021 13:33:52: #2 predicted fragment length is 108 bps INFO @ Sat, 11 Dec 2021 13:33:52: #2 alternative fragment length(s) may be 108 bps INFO @ Sat, 11 Dec 2021 13:33:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386217/SRX10386217.10_model.r INFO @ Sat, 11 Dec 2021 13:33:52: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:33:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:34:14: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:34:16: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:34:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386217/SRX10386217.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:34:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386217/SRX10386217.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:34:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386217/SRX10386217.20_summits.bed INFO @ Sat, 11 Dec 2021 13:34:28: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (682 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:34:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386217/SRX10386217.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:34:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386217/SRX10386217.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:34:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386217/SRX10386217.10_summits.bed INFO @ Sat, 11 Dec 2021 13:34:31: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1034 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。