Job ID = 14172032 SRX = SRX10089744 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 34025331 spots for SRR13700631/SRR13700631.sra Written 34025331 spots for SRR13700631/SRR13700631.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172560 ("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: 00:30:06 34025331 reads; of these: 34025331 (100.00%) were paired; of these: 2851384 (8.38%) aligned concordantly 0 times 27226517 (80.02%) aligned concordantly exactly 1 time 3947430 (11.60%) aligned concordantly >1 times ---- 2851384 pairs aligned concordantly 0 times; of these: 847693 (29.73%) aligned discordantly 1 time ---- 2003691 pairs aligned 0 times concordantly or discordantly; of these: 4007382 mates make up the pairs; of these: 2949450 (73.60%) aligned 0 times 718741 (17.94%) aligned exactly 1 time 339191 (8.46%) aligned >1 times 95.67% overall alignment rate Time searching: 00:30:06 Overall time: 00:30:06 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 24 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] 10846722 / 31577996 = 0.3435 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 14:33:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10089744/SRX10089744.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10089744/SRX10089744.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10089744/SRX10089744.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10089744/SRX10089744.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 14:33:06: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:33:06: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:33:11: 1000000 INFO @ Sat, 11 Dec 2021 14:33:16: 2000000 INFO @ Sat, 11 Dec 2021 14:33:20: 3000000 INFO @ Sat, 11 Dec 2021 14:33:25: 4000000 INFO @ Sat, 11 Dec 2021 14:33:30: 5000000 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 14:33:35: 6000000 INFO @ Sat, 11 Dec 2021 14:33:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10089744/SRX10089744.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10089744/SRX10089744.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10089744/SRX10089744.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10089744/SRX10089744.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 14:33:36: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:33:36: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:33:40: 7000000 INFO @ Sat, 11 Dec 2021 14:33:40: 1000000 INFO @ Sat, 11 Dec 2021 14:33:45: 2000000 INFO @ Sat, 11 Dec 2021 14:33:45: 8000000 INFO @ Sat, 11 Dec 2021 14:33:49: 3000000 INFO @ Sat, 11 Dec 2021 14:33:49: 9000000 INFO @ Sat, 11 Dec 2021 14:33:53: 4000000 INFO @ Sat, 11 Dec 2021 14:33:54: 10000000 INFO @ Sat, 11 Dec 2021 14:33:57: 5000000 INFO @ Sat, 11 Dec 2021 14:33:59: 11000000 INFO @ Sat, 11 Dec 2021 14:34:02: 6000000 INFO @ Sat, 11 Dec 2021 14:34:04: 12000000 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 14:34:06: 7000000 INFO @ Sat, 11 Dec 2021 14:34:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10089744/SRX10089744.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10089744/SRX10089744.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10089744/SRX10089744.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10089744/SRX10089744.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 14:34:06: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:34:06: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:34:09: 13000000 INFO @ Sat, 11 Dec 2021 14:34:10: 8000000 INFO @ Sat, 11 Dec 2021 14:34:10: 1000000 INFO @ Sat, 11 Dec 2021 14:34:13: 14000000 INFO @ Sat, 11 Dec 2021 14:34:14: 9000000 INFO @ Sat, 11 Dec 2021 14:34:15: 2000000 INFO @ Sat, 11 Dec 2021 14:34:18: 15000000 INFO @ Sat, 11 Dec 2021 14:34:19: 10000000 INFO @ Sat, 11 Dec 2021 14:34:19: 3000000 INFO @ Sat, 11 Dec 2021 14:34:23: 11000000 INFO @ Sat, 11 Dec 2021 14:34:23: 16000000 INFO @ Sat, 11 Dec 2021 14:34:23: 4000000 INFO @ Sat, 11 Dec 2021 14:34:27: 12000000 INFO @ Sat, 11 Dec 2021 14:34:28: 5000000 INFO @ Sat, 11 Dec 2021 14:34:28: 17000000 INFO @ Sat, 11 Dec 2021 14:34:31: 13000000 INFO @ Sat, 11 Dec 2021 14:34:32: 6000000 INFO @ Sat, 11 Dec 2021 14:34:33: 18000000 INFO @ Sat, 11 Dec 2021 14:34:36: 14000000 INFO @ Sat, 11 Dec 2021 14:34:36: 7000000 INFO @ Sat, 11 Dec 2021 14:34:37: 19000000 INFO @ Sat, 11 Dec 2021 14:34:40: 15000000 INFO @ Sat, 11 Dec 2021 14:34:40: 8000000 INFO @ Sat, 11 Dec 2021 14:34:42: 20000000 INFO @ Sat, 11 Dec 2021 14:34:44: 16000000 INFO @ Sat, 11 Dec 2021 14:34:45: 9000000 INFO @ Sat, 11 Dec 2021 14:34:47: 21000000 INFO @ Sat, 11 Dec 2021 14:34:48: 17000000 INFO @ Sat, 11 Dec 2021 14:34:49: 10000000 INFO @ Sat, 11 Dec 2021 14:34:52: 22000000 INFO @ Sat, 11 Dec 2021 14:34:53: 18000000 INFO @ Sat, 11 Dec 2021 14:34:53: 11000000 INFO @ Sat, 11 Dec 2021 14:34:56: 23000000 INFO @ Sat, 11 Dec 2021 14:34:57: 19000000 INFO @ Sat, 11 Dec 2021 14:34:58: 12000000 INFO @ Sat, 11 Dec 2021 14:35:01: 24000000 INFO @ Sat, 11 Dec 2021 14:35:01: 20000000 INFO @ Sat, 11 Dec 2021 14:35:02: 13000000 INFO @ Sat, 11 Dec 2021 14:35:05: 21000000 INFO @ Sat, 11 Dec 2021 14:35:06: 25000000 INFO @ Sat, 11 Dec 2021 14:35:06: 14000000 INFO @ Sat, 11 Dec 2021 14:35:10: 22000000 INFO @ Sat, 11 Dec 2021 14:35:10: 15000000 INFO @ Sat, 11 Dec 2021 14:35:11: 26000000 INFO @ Sat, 11 Dec 2021 14:35:14: 23000000 INFO @ Sat, 11 Dec 2021 14:35:15: 16000000 INFO @ Sat, 11 Dec 2021 14:35:16: 27000000 INFO @ Sat, 11 Dec 2021 14:35:18: 24000000 INFO @ Sat, 11 Dec 2021 14:35:19: 17000000 INFO @ Sat, 11 Dec 2021 14:35:20: 28000000 INFO @ Sat, 11 Dec 2021 14:35:23: 25000000 INFO @ Sat, 11 Dec 2021 14:35:23: 18000000 INFO @ Sat, 11 Dec 2021 14:35:25: 29000000 INFO @ Sat, 11 Dec 2021 14:35:27: 26000000 INFO @ Sat, 11 Dec 2021 14:35:28: 19000000 INFO @ Sat, 11 Dec 2021 14:35:30: 30000000 INFO @ Sat, 11 Dec 2021 14:35:31: 27000000 INFO @ Sat, 11 Dec 2021 14:35:32: 20000000 INFO @ Sat, 11 Dec 2021 14:35:35: 31000000 INFO @ Sat, 11 Dec 2021 14:35:36: 28000000 INFO @ Sat, 11 Dec 2021 14:35:36: 21000000 INFO @ Sat, 11 Dec 2021 14:35:40: 32000000 INFO @ Sat, 11 Dec 2021 14:35:40: 22000000 INFO @ Sat, 11 Dec 2021 14:35:40: 29000000 INFO @ Sat, 11 Dec 2021 14:35:44: 23000000 INFO @ Sat, 11 Dec 2021 14:35:45: 33000000 INFO @ Sat, 11 Dec 2021 14:35:45: 30000000 INFO @ Sat, 11 Dec 2021 14:35:49: 24000000 INFO @ Sat, 11 Dec 2021 14:35:49: 31000000 INFO @ Sat, 11 Dec 2021 14:35:50: 34000000 INFO @ Sat, 11 Dec 2021 14:35:53: 25000000 INFO @ Sat, 11 Dec 2021 14:35:53: 32000000 INFO @ Sat, 11 Dec 2021 14:35:54: 35000000 INFO @ Sat, 11 Dec 2021 14:35:57: 26000000 INFO @ Sat, 11 Dec 2021 14:35:58: 33000000 INFO @ Sat, 11 Dec 2021 14:35:59: 36000000 INFO @ Sat, 11 Dec 2021 14:36:02: 27000000 INFO @ Sat, 11 Dec 2021 14:36:02: 34000000 INFO @ Sat, 11 Dec 2021 14:36:04: 37000000 INFO @ Sat, 11 Dec 2021 14:36:06: 28000000 INFO @ Sat, 11 Dec 2021 14:36:06: 35000000 INFO @ Sat, 11 Dec 2021 14:36:09: 38000000 INFO @ Sat, 11 Dec 2021 14:36:10: 29000000 INFO @ Sat, 11 Dec 2021 14:36:11: 36000000 INFO @ Sat, 11 Dec 2021 14:36:14: 39000000 INFO @ Sat, 11 Dec 2021 14:36:15: 30000000 INFO @ Sat, 11 Dec 2021 14:36:15: 37000000 INFO @ Sat, 11 Dec 2021 14:36:19: 40000000 INFO @ Sat, 11 Dec 2021 14:36:19: 31000000 INFO @ Sat, 11 Dec 2021 14:36:20: 38000000 INFO @ Sat, 11 Dec 2021 14:36:23: 32000000 INFO @ Sat, 11 Dec 2021 14:36:24: 41000000 INFO @ Sat, 11 Dec 2021 14:36:24: 39000000 INFO @ Sat, 11 Dec 2021 14:36:28: 33000000 INFO @ Sat, 11 Dec 2021 14:36:28: 40000000 INFO @ Sat, 11 Dec 2021 14:36:28: 42000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:36:32: 34000000 INFO @ Sat, 11 Dec 2021 14:36:32: 41000000 INFO @ Sat, 11 Dec 2021 14:36:33: 43000000 INFO @ Sat, 11 Dec 2021 14:36:35: #1 tag size is determined as 40 bps INFO @ Sat, 11 Dec 2021 14:36:35: #1 tag size = 40 INFO @ Sat, 11 Dec 2021 14:36:35: #1 total tags in treatment: 20423252 INFO @ Sat, 11 Dec 2021 14:36:35: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:36:35: #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 14:36:36: #1 tags after filtering in treatment: 13418654 INFO @ Sat, 11 Dec 2021 14:36:36: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 11 Dec 2021 14:36:36: #1 finished! INFO @ Sat, 11 Dec 2021 14:36:36: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:36:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:36:37: 35000000 INFO @ Sat, 11 Dec 2021 14:36:37: 42000000 INFO @ Sat, 11 Dec 2021 14:36:37: #2 number of paired peaks: 2129 INFO @ Sat, 11 Dec 2021 14:36:37: start model_add_line... INFO @ Sat, 11 Dec 2021 14:36:37: start X-correlation... INFO @ Sat, 11 Dec 2021 14:36:37: end of X-cor INFO @ Sat, 11 Dec 2021 14:36:37: #2 finished! INFO @ Sat, 11 Dec 2021 14:36:37: #2 predicted fragment length is 95 bps INFO @ Sat, 11 Dec 2021 14:36:37: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 11 Dec 2021 14:36:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10089744/SRX10089744.05_model.r INFO @ Sat, 11 Dec 2021 14:36:37: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:36:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:36:41: 43000000 INFO @ Sat, 11 Dec 2021 14:36:41: 36000000 INFO @ Sat, 11 Dec 2021 14:36:43: #1 tag size is determined as 40 bps INFO @ Sat, 11 Dec 2021 14:36:43: #1 tag size = 40 INFO @ Sat, 11 Dec 2021 14:36:43: #1 total tags in treatment: 20423252 INFO @ Sat, 11 Dec 2021 14:36:43: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:36:43: #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 14:36:43: #1 tags after filtering in treatment: 13418654 INFO @ Sat, 11 Dec 2021 14:36:43: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 11 Dec 2021 14:36:43: #1 finished! INFO @ Sat, 11 Dec 2021 14:36:43: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:36:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:36:44: #2 number of paired peaks: 2129 INFO @ Sat, 11 Dec 2021 14:36:44: start model_add_line... INFO @ Sat, 11 Dec 2021 14:36:44: start X-correlation... INFO @ Sat, 11 Dec 2021 14:36:44: end of X-cor INFO @ Sat, 11 Dec 2021 14:36:44: #2 finished! INFO @ Sat, 11 Dec 2021 14:36:44: #2 predicted fragment length is 95 bps INFO @ Sat, 11 Dec 2021 14:36:44: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 11 Dec 2021 14:36:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10089744/SRX10089744.10_model.r INFO @ Sat, 11 Dec 2021 14:36:44: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:36:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:36:45: 37000000 INFO @ Sat, 11 Dec 2021 14:36:50: 38000000 INFO @ Sat, 11 Dec 2021 14:36:54: 39000000 INFO @ Sat, 11 Dec 2021 14:36:58: 40000000 INFO @ Sat, 11 Dec 2021 14:37:02: 41000000 INFO @ Sat, 11 Dec 2021 14:37:03: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:37:06: 42000000 INFO @ Sat, 11 Dec 2021 14:37:10: 43000000 INFO @ Sat, 11 Dec 2021 14:37:11: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:37:12: #1 tag size is determined as 40 bps INFO @ Sat, 11 Dec 2021 14:37:12: #1 tag size = 40 INFO @ Sat, 11 Dec 2021 14:37:12: #1 total tags in treatment: 20423252 INFO @ Sat, 11 Dec 2021 14:37:12: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:37:12: #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 14:37:13: #1 tags after filtering in treatment: 13418654 INFO @ Sat, 11 Dec 2021 14:37:13: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 11 Dec 2021 14:37:13: #1 finished! INFO @ Sat, 11 Dec 2021 14:37:13: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:37:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:37:14: #2 number of paired peaks: 2129 INFO @ Sat, 11 Dec 2021 14:37:14: start model_add_line... INFO @ Sat, 11 Dec 2021 14:37:14: start X-correlation... INFO @ Sat, 11 Dec 2021 14:37:14: end of X-cor INFO @ Sat, 11 Dec 2021 14:37:14: #2 finished! INFO @ Sat, 11 Dec 2021 14:37:14: #2 predicted fragment length is 95 bps INFO @ Sat, 11 Dec 2021 14:37:14: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 11 Dec 2021 14:37:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10089744/SRX10089744.20_model.r INFO @ Sat, 11 Dec 2021 14:37:14: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:37:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:37:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10089744/SRX10089744.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:37:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10089744/SRX10089744.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:37:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10089744/SRX10089744.05_summits.bed INFO @ Sat, 11 Dec 2021 14:37:18: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (16427 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:37:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10089744/SRX10089744.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:37:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10089744/SRX10089744.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:37:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10089744/SRX10089744.10_summits.bed INFO @ Sat, 11 Dec 2021 14:37:24: Done! BigWig に変換しました。 pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10475 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:37:40: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:37:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10089744/SRX10089744.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:37:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10089744/SRX10089744.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:37:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10089744/SRX10089744.20_summits.bed INFO @ Sat, 11 Dec 2021 14:37:54: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4234 records, 4 fields): 5 millis CompletedMACS2peakCalling