Job ID = 6626519 SRX = SRX5736493 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 20558158 spots for SRR8956904/SRR8956904.sra Written 20558158 spots for SRR8956904/SRR8956904.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626721 ("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: 00:28:33 20558158 reads; of these: 20558158 (100.00%) were paired; of these: 2437525 (11.86%) aligned concordantly 0 times 15745659 (76.59%) aligned concordantly exactly 1 time 2374974 (11.55%) aligned concordantly >1 times ---- 2437525 pairs aligned concordantly 0 times; of these: 656809 (26.95%) aligned discordantly 1 time ---- 1780716 pairs aligned 0 times concordantly or discordantly; of these: 3561432 mates make up the pairs; of these: 2744664 (77.07%) aligned 0 times 466532 (13.10%) aligned exactly 1 time 350236 (9.83%) aligned >1 times 93.32% overall alignment rate Time searching: 00:28:33 Overall time: 00:28:33 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 16 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] 1760070 / 18765821 = 0.0938 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 @ Tue, 14 Jul 2020 07:58:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736493/SRX5736493.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736493/SRX5736493.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736493/SRX5736493.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736493/SRX5736493.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 @ Tue, 14 Jul 2020 07:58:38: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:58:38: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:58:44: 1000000 INFO @ Tue, 14 Jul 2020 07:58:49: 2000000 INFO @ Tue, 14 Jul 2020 07:58:54: 3000000 INFO @ Tue, 14 Jul 2020 07:59:00: 4000000 INFO @ Tue, 14 Jul 2020 07:59:05: 5000000 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 @ Tue, 14 Jul 2020 07:59:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736493/SRX5736493.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736493/SRX5736493.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736493/SRX5736493.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736493/SRX5736493.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 @ Tue, 14 Jul 2020 07:59:08: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:59:08: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:59:10: 6000000 INFO @ Tue, 14 Jul 2020 07:59:14: 1000000 INFO @ Tue, 14 Jul 2020 07:59:16: 7000000 INFO @ Tue, 14 Jul 2020 07:59:20: 2000000 INFO @ Tue, 14 Jul 2020 07:59:22: 8000000 INFO @ Tue, 14 Jul 2020 07:59:26: 3000000 INFO @ Tue, 14 Jul 2020 07:59:28: 9000000 INFO @ Tue, 14 Jul 2020 07:59:32: 4000000 INFO @ Tue, 14 Jul 2020 07:59:34: 10000000 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 @ Tue, 14 Jul 2020 07:59:37: 5000000 INFO @ Tue, 14 Jul 2020 07:59:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736493/SRX5736493.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736493/SRX5736493.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736493/SRX5736493.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736493/SRX5736493.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 @ Tue, 14 Jul 2020 07:59:38: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:59:38: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:59:40: 11000000 INFO @ Tue, 14 Jul 2020 07:59:44: 6000000 INFO @ Tue, 14 Jul 2020 07:59:46: 1000000 INFO @ Tue, 14 Jul 2020 07:59:47: 12000000 INFO @ Tue, 14 Jul 2020 07:59:50: 7000000 INFO @ Tue, 14 Jul 2020 07:59:53: 13000000 INFO @ Tue, 14 Jul 2020 07:59:53: 2000000 INFO @ Tue, 14 Jul 2020 07:59:57: 8000000 INFO @ Tue, 14 Jul 2020 08:00:00: 14000000 INFO @ Tue, 14 Jul 2020 08:00:01: 3000000 INFO @ Tue, 14 Jul 2020 08:00:03: 9000000 INFO @ Tue, 14 Jul 2020 08:00:06: 15000000 INFO @ Tue, 14 Jul 2020 08:00:08: 4000000 INFO @ Tue, 14 Jul 2020 08:00:09: 10000000 INFO @ Tue, 14 Jul 2020 08:00:13: 16000000 INFO @ Tue, 14 Jul 2020 08:00:15: 5000000 INFO @ Tue, 14 Jul 2020 08:00:16: 11000000 INFO @ Tue, 14 Jul 2020 08:00:19: 17000000 INFO @ Tue, 14 Jul 2020 08:00:22: 12000000 INFO @ Tue, 14 Jul 2020 08:00:23: 6000000 INFO @ Tue, 14 Jul 2020 08:00:26: 18000000 INFO @ Tue, 14 Jul 2020 08:00:28: 13000000 INFO @ Tue, 14 Jul 2020 08:00:30: 7000000 INFO @ Tue, 14 Jul 2020 08:00:32: 19000000 INFO @ Tue, 14 Jul 2020 08:00:35: 14000000 INFO @ Tue, 14 Jul 2020 08:00:38: 8000000 INFO @ Tue, 14 Jul 2020 08:00:39: 20000000 INFO @ Tue, 14 Jul 2020 08:00:41: 15000000 INFO @ Tue, 14 Jul 2020 08:00:45: 9000000 INFO @ Tue, 14 Jul 2020 08:00:45: 21000000 INFO @ Tue, 14 Jul 2020 08:00:48: 16000000 INFO @ Tue, 14 Jul 2020 08:00:52: 22000000 INFO @ Tue, 14 Jul 2020 08:00:52: 10000000 INFO @ Tue, 14 Jul 2020 08:00:54: 17000000 INFO @ Tue, 14 Jul 2020 08:00:58: 23000000 INFO @ Tue, 14 Jul 2020 08:01:00: 11000000 INFO @ Tue, 14 Jul 2020 08:01:01: 18000000 INFO @ Tue, 14 Jul 2020 08:01:05: 24000000 INFO @ Tue, 14 Jul 2020 08:01:07: 12000000 INFO @ Tue, 14 Jul 2020 08:01:07: 19000000 INFO @ Tue, 14 Jul 2020 08:01:11: 25000000 INFO @ Tue, 14 Jul 2020 08:01:14: 20000000 INFO @ Tue, 14 Jul 2020 08:01:14: 13000000 INFO @ Tue, 14 Jul 2020 08:01:18: 26000000 INFO @ Tue, 14 Jul 2020 08:01:21: 21000000 INFO @ Tue, 14 Jul 2020 08:01:22: 14000000 INFO @ Tue, 14 Jul 2020 08:01:25: 27000000 INFO @ Tue, 14 Jul 2020 08:01:27: 22000000 INFO @ Tue, 14 Jul 2020 08:01:29: 15000000 INFO @ Tue, 14 Jul 2020 08:01:31: 28000000 INFO @ Tue, 14 Jul 2020 08:01:33: 23000000 INFO @ Tue, 14 Jul 2020 08:01:37: 16000000 INFO @ Tue, 14 Jul 2020 08:01:38: 29000000 INFO @ Tue, 14 Jul 2020 08:01:40: 24000000 INFO @ Tue, 14 Jul 2020 08:01:44: 17000000 INFO @ Tue, 14 Jul 2020 08:01:44: 30000000 INFO @ Tue, 14 Jul 2020 08:01:46: 25000000 INFO @ Tue, 14 Jul 2020 08:01:51: 31000000 INFO @ Tue, 14 Jul 2020 08:01:51: 18000000 INFO @ Tue, 14 Jul 2020 08:01:53: 26000000 INFO @ Tue, 14 Jul 2020 08:01:57: 32000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:01:59: 19000000 INFO @ Tue, 14 Jul 2020 08:01:59: 27000000 INFO @ Tue, 14 Jul 2020 08:02:04: 33000000 INFO @ Tue, 14 Jul 2020 08:02:06: 28000000 INFO @ Tue, 14 Jul 2020 08:02:06: 20000000 INFO @ Tue, 14 Jul 2020 08:02:11: 34000000 INFO @ Tue, 14 Jul 2020 08:02:12: 29000000 INFO @ Tue, 14 Jul 2020 08:02:14: 21000000 INFO @ Tue, 14 Jul 2020 08:02:16: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:02:16: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:02:16: #1 total tags in treatment: 16390906 INFO @ Tue, 14 Jul 2020 08:02:16: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:02:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:02:16: #1 tags after filtering in treatment: 13179223 INFO @ Tue, 14 Jul 2020 08:02:16: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 14 Jul 2020 08:02:16: #1 finished! INFO @ Tue, 14 Jul 2020 08:02:16: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:02:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:02:17: #2 number of paired peaks: 356 WARNING @ Tue, 14 Jul 2020 08:02:17: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Tue, 14 Jul 2020 08:02:17: start model_add_line... INFO @ Tue, 14 Jul 2020 08:02:17: start X-correlation... INFO @ Tue, 14 Jul 2020 08:02:17: end of X-cor INFO @ Tue, 14 Jul 2020 08:02:17: #2 finished! INFO @ Tue, 14 Jul 2020 08:02:17: #2 predicted fragment length is 308 bps INFO @ Tue, 14 Jul 2020 08:02:17: #2 alternative fragment length(s) may be 45,66,193,257,279,308,328,365 bps INFO @ Tue, 14 Jul 2020 08:02:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736493/SRX5736493.05_model.r INFO @ Tue, 14 Jul 2020 08:02:17: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:02:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:02:19: 30000000 INFO @ Tue, 14 Jul 2020 08:02:21: 22000000 INFO @ Tue, 14 Jul 2020 08:02:25: 31000000 INFO @ Tue, 14 Jul 2020 08:02:29: 23000000 INFO @ Tue, 14 Jul 2020 08:02:31: 32000000 INFO @ Tue, 14 Jul 2020 08:02:36: 24000000 INFO @ Tue, 14 Jul 2020 08:02:38: 33000000 INFO @ Tue, 14 Jul 2020 08:02:43: 25000000 INFO @ Tue, 14 Jul 2020 08:02:44: 34000000 INFO @ Tue, 14 Jul 2020 08:02:47: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:02:50: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:02:50: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:02:50: #1 total tags in treatment: 16390906 INFO @ Tue, 14 Jul 2020 08:02:50: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:02:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:02:50: #1 tags after filtering in treatment: 13179223 INFO @ Tue, 14 Jul 2020 08:02:50: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 14 Jul 2020 08:02:50: #1 finished! INFO @ Tue, 14 Jul 2020 08:02:50: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:02:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:02:51: 26000000 INFO @ Tue, 14 Jul 2020 08:02:51: #2 number of paired peaks: 356 WARNING @ Tue, 14 Jul 2020 08:02:51: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Tue, 14 Jul 2020 08:02:51: start model_add_line... INFO @ Tue, 14 Jul 2020 08:02:51: start X-correlation... INFO @ Tue, 14 Jul 2020 08:02:51: end of X-cor INFO @ Tue, 14 Jul 2020 08:02:51: #2 finished! INFO @ Tue, 14 Jul 2020 08:02:51: #2 predicted fragment length is 308 bps INFO @ Tue, 14 Jul 2020 08:02:51: #2 alternative fragment length(s) may be 45,66,193,257,279,308,328,365 bps INFO @ Tue, 14 Jul 2020 08:02:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736493/SRX5736493.10_model.r INFO @ Tue, 14 Jul 2020 08:02:51: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:02:51: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:02:58: 27000000 INFO @ Tue, 14 Jul 2020 08:03:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736493/SRX5736493.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:03:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736493/SRX5736493.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:03:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736493/SRX5736493.05_summits.bed INFO @ Tue, 14 Jul 2020 08:03:01: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2471 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:03:05: 28000000 INFO @ Tue, 14 Jul 2020 08:03:12: 29000000 INFO @ Tue, 14 Jul 2020 08:03:18: 30000000 INFO @ Tue, 14 Jul 2020 08:03:20: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:03:25: 31000000 INFO @ Tue, 14 Jul 2020 08:03:32: 32000000 INFO @ Tue, 14 Jul 2020 08:03:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736493/SRX5736493.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:03:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736493/SRX5736493.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:03:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736493/SRX5736493.10_summits.bed INFO @ Tue, 14 Jul 2020 08:03:34: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (807 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:03:39: 33000000 INFO @ Tue, 14 Jul 2020 08:03:46: 34000000 INFO @ Tue, 14 Jul 2020 08:03:52: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:03:52: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:03:52: #1 total tags in treatment: 16390906 INFO @ Tue, 14 Jul 2020 08:03:52: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:03:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:03:52: #1 tags after filtering in treatment: 13179223 INFO @ Tue, 14 Jul 2020 08:03:52: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 14 Jul 2020 08:03:52: #1 finished! INFO @ Tue, 14 Jul 2020 08:03:52: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:03:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:03:53: #2 number of paired peaks: 356 WARNING @ Tue, 14 Jul 2020 08:03:53: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Tue, 14 Jul 2020 08:03:53: start model_add_line... INFO @ Tue, 14 Jul 2020 08:03:53: start X-correlation... INFO @ Tue, 14 Jul 2020 08:03:53: end of X-cor INFO @ Tue, 14 Jul 2020 08:03:53: #2 finished! INFO @ Tue, 14 Jul 2020 08:03:53: #2 predicted fragment length is 308 bps INFO @ Tue, 14 Jul 2020 08:03:53: #2 alternative fragment length(s) may be 45,66,193,257,279,308,328,365 bps INFO @ Tue, 14 Jul 2020 08:03:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736493/SRX5736493.20_model.r INFO @ Tue, 14 Jul 2020 08:03:53: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:03:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:04:23: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:04:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736493/SRX5736493.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:04:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736493/SRX5736493.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:04:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736493/SRX5736493.20_summits.bed INFO @ Tue, 14 Jul 2020 08:04:36: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (125 records, 4 fields): 1 millis CompletedMACS2peakCalling