Job ID = 12265651 SRX = SRX7277053 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 37522265 spots for SRR10597318/SRR10597318.sra Written 37522265 spots for SRR10597318/SRR10597318.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265950 ("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: 00:32:00 37522265 reads; of these: 37522265 (100.00%) were paired; of these: 1488161 (3.97%) aligned concordantly 0 times 10179445 (27.13%) aligned concordantly exactly 1 time 25854659 (68.90%) aligned concordantly >1 times ---- 1488161 pairs aligned concordantly 0 times; of these: 343620 (23.09%) aligned discordantly 1 time ---- 1144541 pairs aligned 0 times concordantly or discordantly; of these: 2289082 mates make up the pairs; of these: 1119980 (48.93%) aligned 0 times 363984 (15.90%) aligned exactly 1 time 805118 (35.17%) aligned >1 times 98.51% overall alignment rate Time searching: 00:32:00 Overall time: 00:32:00 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] 22555901 / 36286811 = 0.6216 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:41:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277053/SRX7277053.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277053/SRX7277053.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277053/SRX7277053.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277053/SRX7277053.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, 03 Apr 2021 08:41:07: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:41:07: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:41:12: 1000000 INFO @ Sat, 03 Apr 2021 08:41:17: 2000000 INFO @ Sat, 03 Apr 2021 08:41:22: 3000000 INFO @ Sat, 03 Apr 2021 08:41:27: 4000000 INFO @ Sat, 03 Apr 2021 08:41:31: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:41:36: 6000000 INFO @ Sat, 03 Apr 2021 08:41:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277053/SRX7277053.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277053/SRX7277053.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277053/SRX7277053.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277053/SRX7277053.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, 03 Apr 2021 08:41:37: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:41:37: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:41:41: 7000000 INFO @ Sat, 03 Apr 2021 08:41:43: 1000000 INFO @ Sat, 03 Apr 2021 08:41:47: 8000000 INFO @ Sat, 03 Apr 2021 08:41:49: 2000000 INFO @ Sat, 03 Apr 2021 08:41:52: 9000000 INFO @ Sat, 03 Apr 2021 08:41:55: 3000000 INFO @ Sat, 03 Apr 2021 08:41:58: 10000000 INFO @ Sat, 03 Apr 2021 08:42:01: 4000000 INFO @ Sat, 03 Apr 2021 08:42:03: 11000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:42:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277053/SRX7277053.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277053/SRX7277053.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277053/SRX7277053.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277053/SRX7277053.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, 03 Apr 2021 08:42:07: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:42:07: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:42:08: 5000000 INFO @ Sat, 03 Apr 2021 08:42:09: 12000000 INFO @ Sat, 03 Apr 2021 08:42:13: 1000000 INFO @ Sat, 03 Apr 2021 08:42:14: 6000000 INFO @ Sat, 03 Apr 2021 08:42:14: 13000000 INFO @ Sat, 03 Apr 2021 08:42:19: 2000000 INFO @ Sat, 03 Apr 2021 08:42:20: 14000000 INFO @ Sat, 03 Apr 2021 08:42:20: 7000000 INFO @ Sat, 03 Apr 2021 08:42:25: 3000000 INFO @ Sat, 03 Apr 2021 08:42:25: 15000000 INFO @ Sat, 03 Apr 2021 08:42:26: 8000000 INFO @ Sat, 03 Apr 2021 08:42:31: 4000000 INFO @ Sat, 03 Apr 2021 08:42:31: 16000000 INFO @ Sat, 03 Apr 2021 08:42:32: 9000000 INFO @ Sat, 03 Apr 2021 08:42:36: 17000000 INFO @ Sat, 03 Apr 2021 08:42:37: 5000000 INFO @ Sat, 03 Apr 2021 08:42:39: 10000000 INFO @ Sat, 03 Apr 2021 08:42:42: 18000000 INFO @ Sat, 03 Apr 2021 08:42:43: 6000000 INFO @ Sat, 03 Apr 2021 08:42:45: 11000000 INFO @ Sat, 03 Apr 2021 08:42:47: 19000000 INFO @ Sat, 03 Apr 2021 08:42:49: 7000000 INFO @ Sat, 03 Apr 2021 08:42:51: 12000000 INFO @ Sat, 03 Apr 2021 08:42:52: 20000000 INFO @ Sat, 03 Apr 2021 08:42:55: 8000000 INFO @ Sat, 03 Apr 2021 08:42:57: 13000000 INFO @ Sat, 03 Apr 2021 08:42:58: 21000000 INFO @ Sat, 03 Apr 2021 08:43:01: 9000000 INFO @ Sat, 03 Apr 2021 08:43:03: 14000000 INFO @ Sat, 03 Apr 2021 08:43:03: 22000000 INFO @ Sat, 03 Apr 2021 08:43:07: 10000000 INFO @ Sat, 03 Apr 2021 08:43:08: 23000000 INFO @ Sat, 03 Apr 2021 08:43:09: 15000000 INFO @ Sat, 03 Apr 2021 08:43:13: 11000000 INFO @ Sat, 03 Apr 2021 08:43:14: 24000000 INFO @ Sat, 03 Apr 2021 08:43:15: 16000000 INFO @ Sat, 03 Apr 2021 08:43:19: 12000000 INFO @ Sat, 03 Apr 2021 08:43:19: 25000000 INFO @ Sat, 03 Apr 2021 08:43:21: 17000000 INFO @ Sat, 03 Apr 2021 08:43:25: 13000000 INFO @ Sat, 03 Apr 2021 08:43:25: 26000000 INFO @ Sat, 03 Apr 2021 08:43:27: 18000000 INFO @ Sat, 03 Apr 2021 08:43:30: 27000000 INFO @ Sat, 03 Apr 2021 08:43:31: 14000000 INFO @ Sat, 03 Apr 2021 08:43:33: 19000000 INFO @ Sat, 03 Apr 2021 08:43:36: 28000000 INFO @ Sat, 03 Apr 2021 08:43:37: 15000000 INFO @ Sat, 03 Apr 2021 08:43:39: 20000000 INFO @ Sat, 03 Apr 2021 08:43:40: #1 tag size is determined as 36 bps INFO @ Sat, 03 Apr 2021 08:43:40: #1 tag size = 36 INFO @ Sat, 03 Apr 2021 08:43:40: #1 total tags in treatment: 13514683 INFO @ Sat, 03 Apr 2021 08:43:40: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:43:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:43:41: #1 tags after filtering in treatment: 9771789 INFO @ Sat, 03 Apr 2021 08:43:41: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 03 Apr 2021 08:43:41: #1 finished! INFO @ Sat, 03 Apr 2021 08:43:41: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:43:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:43:41: #2 number of paired peaks: 200 WARNING @ Sat, 03 Apr 2021 08:43:41: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Sat, 03 Apr 2021 08:43:41: start model_add_line... INFO @ Sat, 03 Apr 2021 08:43:41: start X-correlation... INFO @ Sat, 03 Apr 2021 08:43:41: end of X-cor INFO @ Sat, 03 Apr 2021 08:43:41: #2 finished! INFO @ Sat, 03 Apr 2021 08:43:41: #2 predicted fragment length is 97 bps INFO @ Sat, 03 Apr 2021 08:43:41: #2 alternative fragment length(s) may be 3,97,575 bps INFO @ Sat, 03 Apr 2021 08:43:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277053/SRX7277053.05_model.r INFO @ Sat, 03 Apr 2021 08:43:41: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:43:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:43:43: 16000000 INFO @ Sat, 03 Apr 2021 08:43:45: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:43:49: 17000000 INFO @ Sat, 03 Apr 2021 08:43:51: 22000000 INFO @ Sat, 03 Apr 2021 08:43:55: 18000000 INFO @ Sat, 03 Apr 2021 08:43:57: 23000000 INFO @ Sat, 03 Apr 2021 08:44:00: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:44:01: 19000000 INFO @ Sat, 03 Apr 2021 08:44:03: 24000000 INFO @ Sat, 03 Apr 2021 08:44:07: 20000000 INFO @ Sat, 03 Apr 2021 08:44:09: 25000000 INFO @ Sat, 03 Apr 2021 08:44:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277053/SRX7277053.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:44:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277053/SRX7277053.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:44:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277053/SRX7277053.05_summits.bed INFO @ Sat, 03 Apr 2021 08:44:11: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3615 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:44:13: 21000000 INFO @ Sat, 03 Apr 2021 08:44:15: 26000000 INFO @ Sat, 03 Apr 2021 08:44:19: 22000000 INFO @ Sat, 03 Apr 2021 08:44:20: 27000000 INFO @ Sat, 03 Apr 2021 08:44:25: 23000000 INFO @ Sat, 03 Apr 2021 08:44:26: 28000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:44:31: 24000000 INFO @ Sat, 03 Apr 2021 08:44:31: #1 tag size is determined as 36 bps INFO @ Sat, 03 Apr 2021 08:44:31: #1 tag size = 36 INFO @ Sat, 03 Apr 2021 08:44:31: #1 total tags in treatment: 13514683 INFO @ Sat, 03 Apr 2021 08:44:31: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:44:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:44:31: #1 tags after filtering in treatment: 9771789 INFO @ Sat, 03 Apr 2021 08:44:31: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 03 Apr 2021 08:44:31: #1 finished! INFO @ Sat, 03 Apr 2021 08:44:31: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:44:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:44:32: #2 number of paired peaks: 200 WARNING @ Sat, 03 Apr 2021 08:44:32: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Sat, 03 Apr 2021 08:44:32: start model_add_line... INFO @ Sat, 03 Apr 2021 08:44:32: start X-correlation... INFO @ Sat, 03 Apr 2021 08:44:32: end of X-cor INFO @ Sat, 03 Apr 2021 08:44:32: #2 finished! INFO @ Sat, 03 Apr 2021 08:44:32: #2 predicted fragment length is 97 bps INFO @ Sat, 03 Apr 2021 08:44:32: #2 alternative fragment length(s) may be 3,97,575 bps INFO @ Sat, 03 Apr 2021 08:44:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277053/SRX7277053.10_model.r INFO @ Sat, 03 Apr 2021 08:44:32: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:44:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:44:37: 25000000 INFO @ Sat, 03 Apr 2021 08:44:43: 26000000 INFO @ Sat, 03 Apr 2021 08:44:48: 27000000 INFO @ Sat, 03 Apr 2021 08:44:52: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:44:54: 28000000 INFO @ Sat, 03 Apr 2021 08:44:59: #1 tag size is determined as 36 bps INFO @ Sat, 03 Apr 2021 08:44:59: #1 tag size = 36 INFO @ Sat, 03 Apr 2021 08:44:59: #1 total tags in treatment: 13514683 INFO @ Sat, 03 Apr 2021 08:44:59: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:44:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:44:59: #1 tags after filtering in treatment: 9771789 INFO @ Sat, 03 Apr 2021 08:44:59: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 03 Apr 2021 08:44:59: #1 finished! INFO @ Sat, 03 Apr 2021 08:44:59: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:44:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:45:00: #2 number of paired peaks: 200 WARNING @ Sat, 03 Apr 2021 08:45:00: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Sat, 03 Apr 2021 08:45:00: start model_add_line... INFO @ Sat, 03 Apr 2021 08:45:00: start X-correlation... INFO @ Sat, 03 Apr 2021 08:45:00: end of X-cor INFO @ Sat, 03 Apr 2021 08:45:00: #2 finished! INFO @ Sat, 03 Apr 2021 08:45:00: #2 predicted fragment length is 97 bps INFO @ Sat, 03 Apr 2021 08:45:00: #2 alternative fragment length(s) may be 3,97,575 bps INFO @ Sat, 03 Apr 2021 08:45:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277053/SRX7277053.20_model.r INFO @ Sat, 03 Apr 2021 08:45:00: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:45:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:45:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277053/SRX7277053.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:45:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277053/SRX7277053.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:45:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277053/SRX7277053.10_summits.bed INFO @ Sat, 03 Apr 2021 08:45:02: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1119 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:45:19: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:45:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277053/SRX7277053.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:45:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277053/SRX7277053.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:45:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277053/SRX7277053.20_summits.bed INFO @ Sat, 03 Apr 2021 08:45:29: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (411 records, 4 fields): 1 millis CompletedMACS2peakCalling