Job ID = 14170552 SRX = SRX9720888 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 12359470 spots for SRR13291878/SRR13291878.sra Written 12359470 spots for SRR13291878/SRR13291878.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170954 ("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: 00:04:10 12359470 reads; of these: 12359470 (100.00%) were unpaired; of these: 720781 (5.83%) aligned 0 times 8046696 (65.11%) aligned exactly 1 time 3591993 (29.06%) aligned >1 times 94.17% overall alignment rate Time searching: 00:04:10 Overall time: 00:04:10 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] 1133980 / 11638689 = 0.0974 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 @ Sat, 11 Dec 2021 07:18:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720888/SRX9720888.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720888/SRX9720888.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720888/SRX9720888.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720888/SRX9720888.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, 11 Dec 2021 07:18:31: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:18:31: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:18:38: 1000000 INFO @ Sat, 11 Dec 2021 07:18:45: 2000000 INFO @ Sat, 11 Dec 2021 07:18:52: 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 @ Sat, 11 Dec 2021 07:18:59: 4000000 INFO @ Sat, 11 Dec 2021 07:19:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720888/SRX9720888.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720888/SRX9720888.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720888/SRX9720888.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720888/SRX9720888.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, 11 Dec 2021 07:19:01: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:19:01: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:19:07: 5000000 INFO @ Sat, 11 Dec 2021 07:19:08: 1000000 INFO @ Sat, 11 Dec 2021 07:19:15: 6000000 INFO @ Sat, 11 Dec 2021 07:19:15: 2000000 INFO @ Sat, 11 Dec 2021 07:19:22: 3000000 INFO @ Sat, 11 Dec 2021 07:19:23: 7000000 INFO @ Sat, 11 Dec 2021 07:19:29: 4000000 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 @ Sat, 11 Dec 2021 07:19:31: 8000000 INFO @ Sat, 11 Dec 2021 07:19:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720888/SRX9720888.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720888/SRX9720888.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720888/SRX9720888.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720888/SRX9720888.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, 11 Dec 2021 07:19:31: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:19:31: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:19:36: 5000000 INFO @ Sat, 11 Dec 2021 07:19:38: 1000000 INFO @ Sat, 11 Dec 2021 07:19:39: 9000000 INFO @ Sat, 11 Dec 2021 07:19:43: 6000000 INFO @ Sat, 11 Dec 2021 07:19:45: 2000000 INFO @ Sat, 11 Dec 2021 07:19:47: 10000000 INFO @ Sat, 11 Dec 2021 07:19:50: 7000000 INFO @ Sat, 11 Dec 2021 07:19:51: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:19:51: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:19:51: #1 total tags in treatment: 10504709 INFO @ Sat, 11 Dec 2021 07:19:51: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:19:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:19:51: #1 tags after filtering in treatment: 10504709 INFO @ Sat, 11 Dec 2021 07:19:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:19:51: #1 finished! INFO @ Sat, 11 Dec 2021 07:19:51: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:19:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:19:52: #2 number of paired peaks: 983 WARNING @ Sat, 11 Dec 2021 07:19:52: Fewer paired peaks (983) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 983 pairs to build model! INFO @ Sat, 11 Dec 2021 07:19:52: start model_add_line... INFO @ Sat, 11 Dec 2021 07:19:52: start X-correlation... INFO @ Sat, 11 Dec 2021 07:19:52: end of X-cor INFO @ Sat, 11 Dec 2021 07:19:52: #2 finished! INFO @ Sat, 11 Dec 2021 07:19:52: #2 predicted fragment length is 216 bps INFO @ Sat, 11 Dec 2021 07:19:52: #2 alternative fragment length(s) may be 216 bps INFO @ Sat, 11 Dec 2021 07:19:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720888/SRX9720888.05_model.r INFO @ Sat, 11 Dec 2021 07:19:52: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:19:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:19:52: 3000000 INFO @ Sat, 11 Dec 2021 07:19:57: 8000000 INFO @ Sat, 11 Dec 2021 07:19:59: 4000000 INFO @ Sat, 11 Dec 2021 07:20:03: 9000000 INFO @ Sat, 11 Dec 2021 07:20:05: 5000000 INFO @ Sat, 11 Dec 2021 07:20:09: 10000000 INFO @ Sat, 11 Dec 2021 07:20:11: 6000000 INFO @ Sat, 11 Dec 2021 07:20:12: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:20:12: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:20:12: #1 total tags in treatment: 10504709 INFO @ Sat, 11 Dec 2021 07:20:12: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:20:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:20:12: #1 tags after filtering in treatment: 10504709 INFO @ Sat, 11 Dec 2021 07:20:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:20:12: #1 finished! INFO @ Sat, 11 Dec 2021 07:20:12: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:20:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:20:13: #2 number of paired peaks: 983 WARNING @ Sat, 11 Dec 2021 07:20:13: Fewer paired peaks (983) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 983 pairs to build model! INFO @ Sat, 11 Dec 2021 07:20:13: start model_add_line... INFO @ Sat, 11 Dec 2021 07:20:13: start X-correlation... INFO @ Sat, 11 Dec 2021 07:20:13: end of X-cor INFO @ Sat, 11 Dec 2021 07:20:13: #2 finished! INFO @ Sat, 11 Dec 2021 07:20:13: #2 predicted fragment length is 216 bps INFO @ Sat, 11 Dec 2021 07:20:13: #2 alternative fragment length(s) may be 216 bps INFO @ Sat, 11 Dec 2021 07:20:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720888/SRX9720888.10_model.r INFO @ Sat, 11 Dec 2021 07:20:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:20:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:20:15: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:20:17: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:20:22: 8000000 INFO @ Sat, 11 Dec 2021 07:20:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720888/SRX9720888.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:20:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720888/SRX9720888.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:20:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720888/SRX9720888.05_summits.bed INFO @ Sat, 11 Dec 2021 07:20:27: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4856 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:20:28: 9000000 INFO @ Sat, 11 Dec 2021 07:20:34: 10000000 INFO @ Sat, 11 Dec 2021 07:20:37: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:20:37: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:20:37: #1 total tags in treatment: 10504709 INFO @ Sat, 11 Dec 2021 07:20:37: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:20:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:20:37: #1 tags after filtering in treatment: 10504709 INFO @ Sat, 11 Dec 2021 07:20:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:20:37: #1 finished! INFO @ Sat, 11 Dec 2021 07:20:37: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:20:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:20:37: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:20:38: #2 number of paired peaks: 983 WARNING @ Sat, 11 Dec 2021 07:20:38: Fewer paired peaks (983) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 983 pairs to build model! INFO @ Sat, 11 Dec 2021 07:20:38: start model_add_line... INFO @ Sat, 11 Dec 2021 07:20:38: start X-correlation... INFO @ Sat, 11 Dec 2021 07:20:38: end of X-cor INFO @ Sat, 11 Dec 2021 07:20:38: #2 finished! INFO @ Sat, 11 Dec 2021 07:20:38: #2 predicted fragment length is 216 bps INFO @ Sat, 11 Dec 2021 07:20:38: #2 alternative fragment length(s) may be 216 bps INFO @ Sat, 11 Dec 2021 07:20:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720888/SRX9720888.20_model.r INFO @ Sat, 11 Dec 2021 07:20:38: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:20:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:20:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720888/SRX9720888.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:20:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720888/SRX9720888.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:20:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720888/SRX9720888.10_summits.bed INFO @ Sat, 11 Dec 2021 07:20:49: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3595 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:21:01: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:21:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720888/SRX9720888.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:21:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720888/SRX9720888.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:21:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720888/SRX9720888.20_summits.bed INFO @ Sat, 11 Dec 2021 07:21:13: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2384 records, 4 fields): 3 millis CompletedMACS2peakCalling