Job ID = 14166974 SRX = SRX7541132 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 30996481 spots for SRR10871138/SRR10871138.sra Written 30996481 spots for SRR10871138/SRR10871138.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167305 ("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: 00:08:05 30996481 reads; of these: 30996481 (100.00%) were unpaired; of these: 11920209 (38.46%) aligned 0 times 15746570 (50.80%) aligned exactly 1 time 3329702 (10.74%) aligned >1 times 61.54% overall alignment rate Time searching: 00:08:07 Overall time: 00:08:07 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 8 files... [bam_rmdupse_core] 5187382 / 19076272 = 0.2719 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 08:35:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7541132/SRX7541132.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7541132/SRX7541132.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7541132/SRX7541132.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7541132/SRX7541132.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 08:35:05: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:35:05: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:35:14: 1000000 INFO @ Fri, 10 Dec 2021 08:35:22: 2000000 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 08:35:31: 3000000 INFO @ Fri, 10 Dec 2021 08:35:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7541132/SRX7541132.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7541132/SRX7541132.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7541132/SRX7541132.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7541132/SRX7541132.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 08:35:34: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:35:34: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:35:38: 4000000 INFO @ Fri, 10 Dec 2021 08:35:43: 1000000 INFO @ Fri, 10 Dec 2021 08:35:47: 5000000 INFO @ Fri, 10 Dec 2021 08:35:51: 2000000 INFO @ Fri, 10 Dec 2021 08:35:55: 6000000 BedGraph に変換中... INFO @ Fri, 10 Dec 2021 08:35:58: 3000000 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 08:36:03: 7000000 INFO @ Fri, 10 Dec 2021 08:36:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7541132/SRX7541132.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7541132/SRX7541132.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7541132/SRX7541132.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7541132/SRX7541132.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 08:36:03: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:36:03: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:36:07: 4000000 INFO @ Fri, 10 Dec 2021 08:36:11: 8000000 INFO @ Fri, 10 Dec 2021 08:36:13: 1000000 INFO @ Fri, 10 Dec 2021 08:36:18: 9000000 INFO @ Fri, 10 Dec 2021 08:36:20: 5000000 INFO @ Fri, 10 Dec 2021 08:36:22: 2000000 INFO @ Fri, 10 Dec 2021 08:36:26: 10000000 INFO @ Fri, 10 Dec 2021 08:36:29: 6000000 INFO @ Fri, 10 Dec 2021 08:36:31: 3000000 INFO @ Fri, 10 Dec 2021 08:36:33: 11000000 INFO @ Fri, 10 Dec 2021 08:36:38: 7000000 INFO @ Fri, 10 Dec 2021 08:36:40: 4000000 INFO @ Fri, 10 Dec 2021 08:36:41: 12000000 INFO @ Fri, 10 Dec 2021 08:36:46: 8000000 INFO @ Fri, 10 Dec 2021 08:36:48: 13000000 INFO @ Fri, 10 Dec 2021 08:36:48: 5000000 INFO @ Fri, 10 Dec 2021 08:36:55: 9000000 INFO @ Fri, 10 Dec 2021 08:36:58: 6000000 INFO @ Fri, 10 Dec 2021 08:37:02: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 08:37:02: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 08:37:02: #1 total tags in treatment: 13888890 INFO @ Fri, 10 Dec 2021 08:37:02: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:37:02: #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 08:37:02: #1 tags after filtering in treatment: 13888890 INFO @ Fri, 10 Dec 2021 08:37:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 08:37:02: #1 finished! INFO @ Fri, 10 Dec 2021 08:37:02: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:37:02: 10000000 INFO @ Fri, 10 Dec 2021 08:37:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:37:03: #2 number of paired peaks: 971 WARNING @ Fri, 10 Dec 2021 08:37:03: Fewer paired peaks (971) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 971 pairs to build model! INFO @ Fri, 10 Dec 2021 08:37:03: start model_add_line... INFO @ Fri, 10 Dec 2021 08:37:03: start X-correlation... INFO @ Fri, 10 Dec 2021 08:37:04: end of X-cor INFO @ Fri, 10 Dec 2021 08:37:04: #2 finished! INFO @ Fri, 10 Dec 2021 08:37:04: #2 predicted fragment length is 238 bps INFO @ Fri, 10 Dec 2021 08:37:04: #2 alternative fragment length(s) may be 238 bps INFO @ Fri, 10 Dec 2021 08:37:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7541132/SRX7541132.05_model.r INFO @ Fri, 10 Dec 2021 08:37:04: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:37:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:37:06: 7000000 INFO @ Fri, 10 Dec 2021 08:37:10: 11000000 INFO @ Fri, 10 Dec 2021 08:37:14: 8000000 INFO @ Fri, 10 Dec 2021 08:37:19: 12000000 INFO @ Fri, 10 Dec 2021 08:37:22: 9000000 INFO @ Fri, 10 Dec 2021 08:37:28: 13000000 INFO @ Fri, 10 Dec 2021 08:37:31: 10000000 INFO @ Fri, 10 Dec 2021 08:37:35: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 08:37:35: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 08:37:35: #1 total tags in treatment: 13888890 INFO @ Fri, 10 Dec 2021 08:37:35: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:37:35: #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 08:37:36: #1 tags after filtering in treatment: 13888890 INFO @ Fri, 10 Dec 2021 08:37:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 08:37:36: #1 finished! INFO @ Fri, 10 Dec 2021 08:37:36: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:37:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:37:37: #2 number of paired peaks: 971 WARNING @ Fri, 10 Dec 2021 08:37:37: Fewer paired peaks (971) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 971 pairs to build model! INFO @ Fri, 10 Dec 2021 08:37:37: start model_add_line... INFO @ Fri, 10 Dec 2021 08:37:37: start X-correlation... INFO @ Fri, 10 Dec 2021 08:37:38: end of X-cor INFO @ Fri, 10 Dec 2021 08:37:38: #2 finished! INFO @ Fri, 10 Dec 2021 08:37:38: #2 predicted fragment length is 238 bps INFO @ Fri, 10 Dec 2021 08:37:38: #2 alternative fragment length(s) may be 238 bps INFO @ Fri, 10 Dec 2021 08:37:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7541132/SRX7541132.10_model.r INFO @ Fri, 10 Dec 2021 08:37:38: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:37:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:37:38: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:37:39: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 08:37:47: 12000000 INFO @ Fri, 10 Dec 2021 08:37:54: 13000000 INFO @ Fri, 10 Dec 2021 08:37:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7541132/SRX7541132.05_peaks.xls INFO @ Fri, 10 Dec 2021 08:37:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7541132/SRX7541132.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:37:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7541132/SRX7541132.05_summits.bed INFO @ Fri, 10 Dec 2021 08:37:59: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6542 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 08:38:01: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 08:38:02: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 08:38:02: #1 total tags in treatment: 13888890 INFO @ Fri, 10 Dec 2021 08:38:02: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:38:02: #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 08:38:02: #1 tags after filtering in treatment: 13888890 INFO @ Fri, 10 Dec 2021 08:38:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 08:38:02: #1 finished! INFO @ Fri, 10 Dec 2021 08:38:02: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:38:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:38:03: #2 number of paired peaks: 971 WARNING @ Fri, 10 Dec 2021 08:38:03: Fewer paired peaks (971) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 971 pairs to build model! INFO @ Fri, 10 Dec 2021 08:38:03: start model_add_line... INFO @ Fri, 10 Dec 2021 08:38:03: start X-correlation... INFO @ Fri, 10 Dec 2021 08:38:03: end of X-cor INFO @ Fri, 10 Dec 2021 08:38:03: #2 finished! INFO @ Fri, 10 Dec 2021 08:38:03: #2 predicted fragment length is 238 bps INFO @ Fri, 10 Dec 2021 08:38:03: #2 alternative fragment length(s) may be 238 bps INFO @ Fri, 10 Dec 2021 08:38:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7541132/SRX7541132.20_model.r INFO @ Fri, 10 Dec 2021 08:38:04: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:38:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:38:13: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 08:38:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7541132/SRX7541132.10_peaks.xls INFO @ Fri, 10 Dec 2021 08:38:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7541132/SRX7541132.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:38:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7541132/SRX7541132.10_summits.bed INFO @ Fri, 10 Dec 2021 08:38:32: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5030 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 08:38:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:39:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7541132/SRX7541132.20_peaks.xls INFO @ Fri, 10 Dec 2021 08:39:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7541132/SRX7541132.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:39:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7541132/SRX7541132.20_summits.bed INFO @ Fri, 10 Dec 2021 08:39:01: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (3115 records, 4 fields): 6 millis CompletedMACS2peakCalling