Job ID = 10166275 SRX = SRX9047373 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 25247292 spots for SRR12558901/SRR12558901.sra Written 25247292 spots for SRR12558901/SRR12558901.sra fastq に変換しました。 bowtie でマッピング中... Your job 10167007 ("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: 00:45:34 25247292 reads; of these: 25247292 (100.00%) were paired; of these: 4317314 (17.10%) aligned concordantly 0 times 15570965 (61.67%) aligned concordantly exactly 1 time 5359013 (21.23%) aligned concordantly >1 times ---- 4317314 pairs aligned concordantly 0 times; of these: 1764002 (40.86%) aligned discordantly 1 time ---- 2553312 pairs aligned 0 times concordantly or discordantly; of these: 5106624 mates make up the pairs; of these: 2531946 (49.58%) aligned 0 times 947544 (18.56%) aligned exactly 1 time 1627134 (31.86%) aligned >1 times 94.99% overall alignment rate Time searching: 00:45:34 Overall time: 00:45:34 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] 2095019 / 22640927 = 0.0925 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 21:42:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9047373/SRX9047373.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9047373/SRX9047373.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9047373/SRX9047373.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9047373/SRX9047373.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 @ Thu, 08 Oct 2020 21:42:57: #1 read tag files... INFO @ Thu, 08 Oct 2020 21:42:57: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 21:43:01: 1000000 INFO @ Thu, 08 Oct 2020 21:43:05: 2000000 INFO @ Thu, 08 Oct 2020 21:43:09: 3000000 INFO @ Thu, 08 Oct 2020 21:43:13: 4000000 INFO @ Thu, 08 Oct 2020 21:43:17: 5000000 INFO @ Thu, 08 Oct 2020 21:43:22: 6000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 21:43:26: 7000000 INFO @ Thu, 08 Oct 2020 21:43:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9047373/SRX9047373.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9047373/SRX9047373.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9047373/SRX9047373.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9047373/SRX9047373.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 @ Thu, 08 Oct 2020 21:43:27: #1 read tag files... INFO @ Thu, 08 Oct 2020 21:43:27: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 21:43:30: 8000000 INFO @ Thu, 08 Oct 2020 21:43:31: 1000000 INFO @ Thu, 08 Oct 2020 21:43:34: 9000000 INFO @ Thu, 08 Oct 2020 21:43:35: 2000000 INFO @ Thu, 08 Oct 2020 21:43:38: 10000000 INFO @ Thu, 08 Oct 2020 21:43:39: 3000000 INFO @ Thu, 08 Oct 2020 21:43:43: 11000000 INFO @ Thu, 08 Oct 2020 21:43:44: 4000000 INFO @ Thu, 08 Oct 2020 21:43:47: 12000000 INFO @ Thu, 08 Oct 2020 21:43:48: 5000000 INFO @ Thu, 08 Oct 2020 21:43:51: 13000000 INFO @ Thu, 08 Oct 2020 21:43:52: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 21:43:55: 14000000 INFO @ Thu, 08 Oct 2020 21:43:56: 7000000 INFO @ Thu, 08 Oct 2020 21:43:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9047373/SRX9047373.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9047373/SRX9047373.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9047373/SRX9047373.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9047373/SRX9047373.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 @ Thu, 08 Oct 2020 21:43:57: #1 read tag files... INFO @ Thu, 08 Oct 2020 21:43:57: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 21:43:59: 15000000 INFO @ Thu, 08 Oct 2020 21:44:01: 8000000 INFO @ Thu, 08 Oct 2020 21:44:01: 1000000 INFO @ Thu, 08 Oct 2020 21:44:04: 16000000 INFO @ Thu, 08 Oct 2020 21:44:05: 9000000 INFO @ Thu, 08 Oct 2020 21:44:05: 2000000 INFO @ Thu, 08 Oct 2020 21:44:08: 17000000 INFO @ Thu, 08 Oct 2020 21:44:09: 10000000 INFO @ Thu, 08 Oct 2020 21:44:10: 3000000 INFO @ Thu, 08 Oct 2020 21:44:12: 18000000 INFO @ Thu, 08 Oct 2020 21:44:13: 11000000 INFO @ Thu, 08 Oct 2020 21:44:14: 4000000 INFO @ Thu, 08 Oct 2020 21:44:17: 19000000 INFO @ Thu, 08 Oct 2020 21:44:18: 12000000 INFO @ Thu, 08 Oct 2020 21:44:18: 5000000 INFO @ Thu, 08 Oct 2020 21:44:21: 20000000 INFO @ Thu, 08 Oct 2020 21:44:22: 13000000 INFO @ Thu, 08 Oct 2020 21:44:22: 6000000 INFO @ Thu, 08 Oct 2020 21:44:25: 21000000 INFO @ Thu, 08 Oct 2020 21:44:26: 14000000 INFO @ Thu, 08 Oct 2020 21:44:27: 7000000 INFO @ Thu, 08 Oct 2020 21:44:29: 22000000 INFO @ Thu, 08 Oct 2020 21:44:31: 15000000 INFO @ Thu, 08 Oct 2020 21:44:31: 8000000 INFO @ Thu, 08 Oct 2020 21:44:34: 23000000 INFO @ Thu, 08 Oct 2020 21:44:35: 16000000 INFO @ Thu, 08 Oct 2020 21:44:35: 9000000 INFO @ Thu, 08 Oct 2020 21:44:38: 24000000 INFO @ Thu, 08 Oct 2020 21:44:39: 17000000 INFO @ Thu, 08 Oct 2020 21:44:40: 10000000 INFO @ Thu, 08 Oct 2020 21:44:42: 25000000 INFO @ Thu, 08 Oct 2020 21:44:43: 18000000 INFO @ Thu, 08 Oct 2020 21:44:44: 11000000 INFO @ Thu, 08 Oct 2020 21:44:46: 26000000 INFO @ Thu, 08 Oct 2020 21:44:48: 19000000 INFO @ Thu, 08 Oct 2020 21:44:48: 12000000 INFO @ Thu, 08 Oct 2020 21:44:51: 27000000 INFO @ Thu, 08 Oct 2020 21:44:52: 20000000 INFO @ Thu, 08 Oct 2020 21:44:52: 13000000 INFO @ Thu, 08 Oct 2020 21:44:55: 28000000 INFO @ Thu, 08 Oct 2020 21:44:56: 21000000 INFO @ Thu, 08 Oct 2020 21:44:57: 14000000 INFO @ Thu, 08 Oct 2020 21:44:59: 29000000 INFO @ Thu, 08 Oct 2020 21:45:01: 22000000 INFO @ Thu, 08 Oct 2020 21:45:01: 15000000 INFO @ Thu, 08 Oct 2020 21:45:03: 30000000 INFO @ Thu, 08 Oct 2020 21:45:05: 23000000 INFO @ Thu, 08 Oct 2020 21:45:05: 16000000 INFO @ Thu, 08 Oct 2020 21:45:08: 31000000 INFO @ Thu, 08 Oct 2020 21:45:09: 24000000 INFO @ Thu, 08 Oct 2020 21:45:09: 17000000 INFO @ Thu, 08 Oct 2020 21:45:12: 32000000 INFO @ Thu, 08 Oct 2020 21:45:13: 25000000 INFO @ Thu, 08 Oct 2020 21:45:14: 18000000 INFO @ Thu, 08 Oct 2020 21:45:16: 33000000 INFO @ Thu, 08 Oct 2020 21:45:18: 26000000 INFO @ Thu, 08 Oct 2020 21:45:18: 19000000 INFO @ Thu, 08 Oct 2020 21:45:20: 34000000 INFO @ Thu, 08 Oct 2020 21:45:22: 27000000 INFO @ Thu, 08 Oct 2020 21:45:22: 20000000 INFO @ Thu, 08 Oct 2020 21:45:25: 35000000 INFO @ Thu, 08 Oct 2020 21:45:26: 28000000 INFO @ Thu, 08 Oct 2020 21:45:26: 21000000 INFO @ Thu, 08 Oct 2020 21:45:29: 36000000 INFO @ Thu, 08 Oct 2020 21:45:30: 29000000 INFO @ Thu, 08 Oct 2020 21:45:31: 22000000 INFO @ Thu, 08 Oct 2020 21:45:33: 37000000 INFO @ Thu, 08 Oct 2020 21:45:35: 30000000 INFO @ Thu, 08 Oct 2020 21:45:35: 23000000 INFO @ Thu, 08 Oct 2020 21:45:38: 38000000 INFO @ Thu, 08 Oct 2020 21:45:39: 31000000 INFO @ Thu, 08 Oct 2020 21:45:39: 24000000 INFO @ Thu, 08 Oct 2020 21:45:42: 39000000 INFO @ Thu, 08 Oct 2020 21:45:43: 32000000 INFO @ Thu, 08 Oct 2020 21:45:44: 25000000 INFO @ Thu, 08 Oct 2020 21:45:46: 40000000 INFO @ Thu, 08 Oct 2020 21:45:48: 33000000 INFO @ Thu, 08 Oct 2020 21:45:48: 26000000 INFO @ Thu, 08 Oct 2020 21:45:50: 41000000 INFO @ Thu, 08 Oct 2020 21:45:52: 34000000 INFO @ Thu, 08 Oct 2020 21:45:52: 27000000 INFO @ Thu, 08 Oct 2020 21:45:55: 42000000 INFO @ Thu, 08 Oct 2020 21:45:56: 35000000 INFO @ Thu, 08 Oct 2020 21:45:56: 28000000 INFO @ Thu, 08 Oct 2020 21:45:59: 43000000 INFO @ Thu, 08 Oct 2020 21:46:00: 36000000 INFO @ Thu, 08 Oct 2020 21:46:01: 29000000 INFO @ Thu, 08 Oct 2020 21:46:02: #1 tag size is determined as 42 bps INFO @ Thu, 08 Oct 2020 21:46:02: #1 tag size = 42 INFO @ Thu, 08 Oct 2020 21:46:02: #1 total tags in treatment: 18941907 INFO @ Thu, 08 Oct 2020 21:46:02: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 21:46:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 21:46:03: #1 tags after filtering in treatment: 15892788 INFO @ Thu, 08 Oct 2020 21:46:03: #1 Redundant rate of treatment: 0.16 INFO @ Thu, 08 Oct 2020 21:46:03: #1 finished! INFO @ Thu, 08 Oct 2020 21:46:03: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 21:46:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 21:46:04: #2 number of paired peaks: 1773 INFO @ Thu, 08 Oct 2020 21:46:04: start model_add_line... INFO @ Thu, 08 Oct 2020 21:46:04: start X-correlation... INFO @ Thu, 08 Oct 2020 21:46:04: end of X-cor INFO @ Thu, 08 Oct 2020 21:46:04: #2 finished! INFO @ Thu, 08 Oct 2020 21:46:04: #2 predicted fragment length is 282 bps INFO @ Thu, 08 Oct 2020 21:46:04: #2 alternative fragment length(s) may be 282 bps INFO @ Thu, 08 Oct 2020 21:46:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9047373/SRX9047373.05_model.r INFO @ Thu, 08 Oct 2020 21:46:04: #3 Call peaks... INFO @ Thu, 08 Oct 2020 21:46:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 21:46:05: 37000000 INFO @ Thu, 08 Oct 2020 21:46:05: 30000000 INFO @ Thu, 08 Oct 2020 21:46:09: 38000000 INFO @ Thu, 08 Oct 2020 21:46:09: 31000000 INFO @ Thu, 08 Oct 2020 21:46:13: 39000000 INFO @ Thu, 08 Oct 2020 21:46:14: 32000000 INFO @ Thu, 08 Oct 2020 21:46:18: 40000000 INFO @ Thu, 08 Oct 2020 21:46:18: 33000000 INFO @ Thu, 08 Oct 2020 21:46:22: 41000000 INFO @ Thu, 08 Oct 2020 21:46:22: 34000000 INFO @ Thu, 08 Oct 2020 21:46:26: 42000000 INFO @ Thu, 08 Oct 2020 21:46:27: 35000000 INFO @ Thu, 08 Oct 2020 21:46:30: 43000000 INFO @ Thu, 08 Oct 2020 21:46:31: 36000000 INFO @ Thu, 08 Oct 2020 21:46:34: #1 tag size is determined as 42 bps INFO @ Thu, 08 Oct 2020 21:46:34: #1 tag size = 42 INFO @ Thu, 08 Oct 2020 21:46:34: #1 total tags in treatment: 18941907 INFO @ Thu, 08 Oct 2020 21:46:34: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 21:46:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 21:46:34: #1 tags after filtering in treatment: 15892788 INFO @ Thu, 08 Oct 2020 21:46:34: #1 Redundant rate of treatment: 0.16 INFO @ Thu, 08 Oct 2020 21:46:34: #1 finished! INFO @ Thu, 08 Oct 2020 21:46:34: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 21:46:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 21:46:35: 37000000 INFO @ Thu, 08 Oct 2020 21:46:35: #2 number of paired peaks: 1773 INFO @ Thu, 08 Oct 2020 21:46:35: start model_add_line... INFO @ Thu, 08 Oct 2020 21:46:36: start X-correlation... INFO @ Thu, 08 Oct 2020 21:46:36: end of X-cor INFO @ Thu, 08 Oct 2020 21:46:36: #2 finished! INFO @ Thu, 08 Oct 2020 21:46:36: #2 predicted fragment length is 282 bps INFO @ Thu, 08 Oct 2020 21:46:36: #2 alternative fragment length(s) may be 282 bps INFO @ Thu, 08 Oct 2020 21:46:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9047373/SRX9047373.10_model.r INFO @ Thu, 08 Oct 2020 21:46:36: #3 Call peaks... INFO @ Thu, 08 Oct 2020 21:46:36: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 21:46:40: 38000000 INFO @ Thu, 08 Oct 2020 21:46:44: 39000000 INFO @ Thu, 08 Oct 2020 21:46:48: 40000000 INFO @ Thu, 08 Oct 2020 21:46:48: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 21:46:52: 41000000 INFO @ Thu, 08 Oct 2020 21:46:57: 42000000 INFO @ Thu, 08 Oct 2020 21:47:01: 43000000 INFO @ Thu, 08 Oct 2020 21:47:04: #1 tag size is determined as 42 bps INFO @ Thu, 08 Oct 2020 21:47:04: #1 tag size = 42 INFO @ Thu, 08 Oct 2020 21:47:04: #1 total tags in treatment: 18941907 INFO @ Thu, 08 Oct 2020 21:47:04: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 21:47:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 21:47:05: #1 tags after filtering in treatment: 15892788 INFO @ Thu, 08 Oct 2020 21:47:05: #1 Redundant rate of treatment: 0.16 INFO @ Thu, 08 Oct 2020 21:47:05: #1 finished! INFO @ Thu, 08 Oct 2020 21:47:05: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 21:47:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 21:47:06: #2 number of paired peaks: 1773 INFO @ Thu, 08 Oct 2020 21:47:06: start model_add_line... INFO @ Thu, 08 Oct 2020 21:47:06: start X-correlation... INFO @ Thu, 08 Oct 2020 21:47:06: end of X-cor INFO @ Thu, 08 Oct 2020 21:47:06: #2 finished! INFO @ Thu, 08 Oct 2020 21:47:06: #2 predicted fragment length is 282 bps INFO @ Thu, 08 Oct 2020 21:47:06: #2 alternative fragment length(s) may be 282 bps INFO @ Thu, 08 Oct 2020 21:47:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9047373/SRX9047373.20_model.r INFO @ Thu, 08 Oct 2020 21:47:06: #3 Call peaks... INFO @ Thu, 08 Oct 2020 21:47:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 21:47:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9047373/SRX9047373.05_peaks.xls INFO @ Thu, 08 Oct 2020 21:47:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9047373/SRX9047373.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 21:47:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9047373/SRX9047373.05_summits.bed INFO @ Thu, 08 Oct 2020 21:47:07: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (8253 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 21:47:19: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 21:47:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9047373/SRX9047373.10_peaks.xls INFO @ Thu, 08 Oct 2020 21:47:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9047373/SRX9047373.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 21:47:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9047373/SRX9047373.10_summits.bed INFO @ Thu, 08 Oct 2020 21:47:38: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6377 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 21:47:49: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 21:48:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9047373/SRX9047373.20_peaks.xls INFO @ Thu, 08 Oct 2020 21:48:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9047373/SRX9047373.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 21:48:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9047373/SRX9047373.20_summits.bed INFO @ Thu, 08 Oct 2020 21:48:07: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4284 records, 4 fields): 6 millis CompletedMACS2peakCalling