Job ID = 14167256 SRX = SRX7848953 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 49967250 spots for SRR11237236/SRR11237236.sra Written 49967250 spots for SRR11237236/SRR11237236.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167910 ("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: 00:16:09 49967250 reads; of these: 49967250 (100.00%) were unpaired; of these: 2765971 (5.54%) aligned 0 times 33147896 (66.34%) aligned exactly 1 time 14053383 (28.13%) aligned >1 times 94.46% overall alignment rate Time searching: 00:16:09 Overall time: 00:16:09 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_rmdupse_core] 14281139 / 47201279 = 0.3026 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 @ Fri, 10 Dec 2021 11:47:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7848953/SRX7848953.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7848953/SRX7848953.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7848953/SRX7848953.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7848953/SRX7848953.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 @ Fri, 10 Dec 2021 11:47:11: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:47:11: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:47:18: 1000000 INFO @ Fri, 10 Dec 2021 11:47:25: 2000000 INFO @ Fri, 10 Dec 2021 11:47:32: 3000000 INFO @ Fri, 10 Dec 2021 11:47:38: 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 @ Fri, 10 Dec 2021 11:47:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7848953/SRX7848953.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7848953/SRX7848953.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7848953/SRX7848953.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7848953/SRX7848953.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 @ Fri, 10 Dec 2021 11:47:41: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:47:41: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:47:45: 5000000 INFO @ Fri, 10 Dec 2021 11:47:49: 1000000 INFO @ Fri, 10 Dec 2021 11:47:52: 6000000 INFO @ Fri, 10 Dec 2021 11:47:56: 2000000 INFO @ Fri, 10 Dec 2021 11:48:00: 7000000 INFO @ Fri, 10 Dec 2021 11:48:03: 3000000 INFO @ Fri, 10 Dec 2021 11:48:07: 8000000 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 @ Fri, 10 Dec 2021 11:48:11: 4000000 INFO @ Fri, 10 Dec 2021 11:48:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7848953/SRX7848953.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7848953/SRX7848953.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7848953/SRX7848953.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7848953/SRX7848953.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 @ Fri, 10 Dec 2021 11:48:11: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:48:11: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:48:14: 9000000 INFO @ Fri, 10 Dec 2021 11:48:18: 5000000 INFO @ Fri, 10 Dec 2021 11:48:19: 1000000 INFO @ Fri, 10 Dec 2021 11:48:22: 10000000 INFO @ Fri, 10 Dec 2021 11:48:25: 6000000 INFO @ Fri, 10 Dec 2021 11:48:27: 2000000 INFO @ Fri, 10 Dec 2021 11:48:29: 11000000 INFO @ Fri, 10 Dec 2021 11:48:33: 7000000 INFO @ Fri, 10 Dec 2021 11:48:35: 3000000 INFO @ Fri, 10 Dec 2021 11:48:37: 12000000 INFO @ Fri, 10 Dec 2021 11:48:40: 8000000 INFO @ Fri, 10 Dec 2021 11:48:42: 4000000 INFO @ Fri, 10 Dec 2021 11:48:44: 13000000 INFO @ Fri, 10 Dec 2021 11:48:48: 9000000 INFO @ Fri, 10 Dec 2021 11:48:50: 5000000 INFO @ Fri, 10 Dec 2021 11:48:52: 14000000 INFO @ Fri, 10 Dec 2021 11:48:55: 10000000 INFO @ Fri, 10 Dec 2021 11:48:57: 6000000 INFO @ Fri, 10 Dec 2021 11:48:59: 15000000 INFO @ Fri, 10 Dec 2021 11:49:02: 11000000 INFO @ Fri, 10 Dec 2021 11:49:05: 7000000 INFO @ Fri, 10 Dec 2021 11:49:07: 16000000 INFO @ Fri, 10 Dec 2021 11:49:10: 12000000 INFO @ Fri, 10 Dec 2021 11:49:12: 8000000 INFO @ Fri, 10 Dec 2021 11:49:14: 17000000 INFO @ Fri, 10 Dec 2021 11:49:17: 13000000 INFO @ Fri, 10 Dec 2021 11:49:20: 9000000 INFO @ Fri, 10 Dec 2021 11:49:22: 18000000 INFO @ Fri, 10 Dec 2021 11:49:25: 14000000 INFO @ Fri, 10 Dec 2021 11:49:28: 10000000 INFO @ Fri, 10 Dec 2021 11:49:29: 19000000 INFO @ Fri, 10 Dec 2021 11:49:32: 15000000 INFO @ Fri, 10 Dec 2021 11:49:35: 11000000 INFO @ Fri, 10 Dec 2021 11:49:37: 20000000 INFO @ Fri, 10 Dec 2021 11:49:39: 16000000 INFO @ Fri, 10 Dec 2021 11:49:43: 12000000 INFO @ Fri, 10 Dec 2021 11:49:44: 21000000 INFO @ Fri, 10 Dec 2021 11:49:47: 17000000 INFO @ Fri, 10 Dec 2021 11:49:50: 13000000 INFO @ Fri, 10 Dec 2021 11:49:52: 22000000 INFO @ Fri, 10 Dec 2021 11:49:54: 18000000 INFO @ Fri, 10 Dec 2021 11:49:58: 14000000 INFO @ Fri, 10 Dec 2021 11:49:59: 23000000 INFO @ Fri, 10 Dec 2021 11:50:02: 19000000 INFO @ Fri, 10 Dec 2021 11:50:05: 15000000 INFO @ Fri, 10 Dec 2021 11:50:07: 24000000 INFO @ Fri, 10 Dec 2021 11:50:09: 20000000 INFO @ Fri, 10 Dec 2021 11:50:13: 16000000 INFO @ Fri, 10 Dec 2021 11:50:14: 25000000 INFO @ Fri, 10 Dec 2021 11:50:16: 21000000 INFO @ Fri, 10 Dec 2021 11:50:21: 17000000 INFO @ Fri, 10 Dec 2021 11:50:22: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:50:24: 22000000 INFO @ Fri, 10 Dec 2021 11:50:28: 18000000 INFO @ Fri, 10 Dec 2021 11:50:30: 27000000 INFO @ Fri, 10 Dec 2021 11:50:31: 23000000 INFO @ Fri, 10 Dec 2021 11:50:36: 19000000 INFO @ Fri, 10 Dec 2021 11:50:37: 28000000 INFO @ Fri, 10 Dec 2021 11:50:39: 24000000 INFO @ Fri, 10 Dec 2021 11:50:43: 20000000 INFO @ Fri, 10 Dec 2021 11:50:45: 29000000 INFO @ Fri, 10 Dec 2021 11:50:47: 25000000 INFO @ Fri, 10 Dec 2021 11:50:51: 21000000 INFO @ Fri, 10 Dec 2021 11:50:52: 30000000 INFO @ Fri, 10 Dec 2021 11:50:54: 26000000 INFO @ Fri, 10 Dec 2021 11:50:59: 22000000 INFO @ Fri, 10 Dec 2021 11:51:00: 31000000 INFO @ Fri, 10 Dec 2021 11:51:02: 27000000 INFO @ Fri, 10 Dec 2021 11:51:06: 23000000 INFO @ Fri, 10 Dec 2021 11:51:07: 32000000 INFO @ Fri, 10 Dec 2021 11:51:09: 28000000 INFO @ Fri, 10 Dec 2021 11:51:14: 24000000 INFO @ Fri, 10 Dec 2021 11:51:14: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 11:51:14: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 11:51:14: #1 total tags in treatment: 32920140 INFO @ Fri, 10 Dec 2021 11:51:14: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:51:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:51:15: #1 tags after filtering in treatment: 32920140 INFO @ Fri, 10 Dec 2021 11:51:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:51:15: #1 finished! INFO @ Fri, 10 Dec 2021 11:51:15: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:51:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:51:17: 29000000 INFO @ Fri, 10 Dec 2021 11:51:17: #2 number of paired peaks: 128 WARNING @ Fri, 10 Dec 2021 11:51:17: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Fri, 10 Dec 2021 11:51:17: start model_add_line... INFO @ Fri, 10 Dec 2021 11:51:17: start X-correlation... INFO @ Fri, 10 Dec 2021 11:51:17: end of X-cor INFO @ Fri, 10 Dec 2021 11:51:17: #2 finished! INFO @ Fri, 10 Dec 2021 11:51:17: #2 predicted fragment length is 128 bps INFO @ Fri, 10 Dec 2021 11:51:17: #2 alternative fragment length(s) may be 3,112,128 bps INFO @ Fri, 10 Dec 2021 11:51:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7848953/SRX7848953.05_model.r INFO @ Fri, 10 Dec 2021 11:51:17: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:51:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:51:21: 25000000 INFO @ Fri, 10 Dec 2021 11:51:24: 30000000 INFO @ Fri, 10 Dec 2021 11:51:29: 26000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:51:31: 31000000 INFO @ Fri, 10 Dec 2021 11:51:37: 27000000 INFO @ Fri, 10 Dec 2021 11:51:39: 32000000 INFO @ Fri, 10 Dec 2021 11:51:44: 28000000 INFO @ Fri, 10 Dec 2021 11:51:46: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 11:51:46: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 11:51:46: #1 total tags in treatment: 32920140 INFO @ Fri, 10 Dec 2021 11:51:46: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:51:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:51:46: #1 tags after filtering in treatment: 32920140 INFO @ Fri, 10 Dec 2021 11:51:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:51:46: #1 finished! INFO @ Fri, 10 Dec 2021 11:51:46: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:51:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:51:48: #2 number of paired peaks: 128 WARNING @ Fri, 10 Dec 2021 11:51:48: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Fri, 10 Dec 2021 11:51:48: start model_add_line... INFO @ Fri, 10 Dec 2021 11:51:48: start X-correlation... INFO @ Fri, 10 Dec 2021 11:51:49: end of X-cor INFO @ Fri, 10 Dec 2021 11:51:49: #2 finished! INFO @ Fri, 10 Dec 2021 11:51:49: #2 predicted fragment length is 128 bps INFO @ Fri, 10 Dec 2021 11:51:49: #2 alternative fragment length(s) may be 3,112,128 bps INFO @ Fri, 10 Dec 2021 11:51:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7848953/SRX7848953.10_model.r INFO @ Fri, 10 Dec 2021 11:51:49: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:51:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:51:51: 29000000 INFO @ Fri, 10 Dec 2021 11:51:58: 30000000 INFO @ Fri, 10 Dec 2021 11:52:05: 31000000 INFO @ Fri, 10 Dec 2021 11:52:12: 32000000 INFO @ Fri, 10 Dec 2021 11:52:15: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:52:18: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 11:52:18: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 11:52:18: #1 total tags in treatment: 32920140 INFO @ Fri, 10 Dec 2021 11:52:18: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:52:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:52:18: #1 tags after filtering in treatment: 32920140 INFO @ Fri, 10 Dec 2021 11:52:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:52:18: #1 finished! INFO @ Fri, 10 Dec 2021 11:52:18: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:52:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:52:20: #2 number of paired peaks: 128 WARNING @ Fri, 10 Dec 2021 11:52:20: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Fri, 10 Dec 2021 11:52:20: start model_add_line... INFO @ Fri, 10 Dec 2021 11:52:20: start X-correlation... INFO @ Fri, 10 Dec 2021 11:52:20: end of X-cor INFO @ Fri, 10 Dec 2021 11:52:20: #2 finished! INFO @ Fri, 10 Dec 2021 11:52:20: #2 predicted fragment length is 128 bps INFO @ Fri, 10 Dec 2021 11:52:20: #2 alternative fragment length(s) may be 3,112,128 bps INFO @ Fri, 10 Dec 2021 11:52:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7848953/SRX7848953.20_model.r INFO @ Fri, 10 Dec 2021 11:52:21: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:52:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:52:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7848953/SRX7848953.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:52:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7848953/SRX7848953.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:52:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7848953/SRX7848953.05_summits.bed INFO @ Fri, 10 Dec 2021 11:52:43: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7953 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:52:47: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:53:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7848953/SRX7848953.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:53:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7848953/SRX7848953.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:53:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7848953/SRX7848953.10_summits.bed INFO @ Fri, 10 Dec 2021 11:53:15: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4470 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:53:19: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:53:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7848953/SRX7848953.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:53:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7848953/SRX7848953.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:53:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7848953/SRX7848953.20_summits.bed INFO @ Fri, 10 Dec 2021 11:53:47: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2035 records, 4 fields): 4 millis CompletedMACS2peakCalling