Job ID = 14170583 SRX = SRX9372360 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12880083 spots for SRR12907637/SRR12907637.sra Written 12880083 spots for SRR12907637/SRR12907637.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171013 ("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: 00:11:03 12880083 reads; of these: 12880083 (100.00%) were paired; of these: 7261660 (56.38%) aligned concordantly 0 times 4267730 (33.13%) aligned concordantly exactly 1 time 1350693 (10.49%) aligned concordantly >1 times ---- 7261660 pairs aligned concordantly 0 times; of these: 295971 (4.08%) aligned discordantly 1 time ---- 6965689 pairs aligned 0 times concordantly or discordantly; of these: 13931378 mates make up the pairs; of these: 13260593 (95.19%) aligned 0 times 404320 (2.90%) aligned exactly 1 time 266465 (1.91%) aligned >1 times 48.52% overall alignment rate Time searching: 00:11:03 Overall time: 00:11:03 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_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] 339771 / 5906999 = 0.0575 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 07:34:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9372360/SRX9372360.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9372360/SRX9372360.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9372360/SRX9372360.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9372360/SRX9372360.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 07:34:47: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:34:47: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:34:52: 1000000 INFO @ Sat, 11 Dec 2021 07:34:57: 2000000 INFO @ Sat, 11 Dec 2021 07:35:02: 3000000 INFO @ Sat, 11 Dec 2021 07:35:07: 4000000 INFO @ Sat, 11 Dec 2021 07:35:12: 5000000 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 07:35:17: 6000000 INFO @ Sat, 11 Dec 2021 07:35:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9372360/SRX9372360.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9372360/SRX9372360.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9372360/SRX9372360.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9372360/SRX9372360.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 07:35:17: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:35:17: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:35:22: 7000000 INFO @ Sat, 11 Dec 2021 07:35:22: 1000000 INFO @ Sat, 11 Dec 2021 07:35:27: 8000000 INFO @ Sat, 11 Dec 2021 07:35:28: 2000000 INFO @ Sat, 11 Dec 2021 07:35:32: 9000000 INFO @ Sat, 11 Dec 2021 07:35:33: 3000000 INFO @ Sat, 11 Dec 2021 07:35:37: 10000000 INFO @ Sat, 11 Dec 2021 07:35:38: 4000000 INFO @ Sat, 11 Dec 2021 07:35:43: 11000000 INFO @ Sat, 11 Dec 2021 07:35:43: 5000000 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 07:35:47: #1 tag size is determined as 43 bps INFO @ Sat, 11 Dec 2021 07:35:47: #1 tag size = 43 INFO @ Sat, 11 Dec 2021 07:35:47: #1 total tags in treatment: 5292100 INFO @ Sat, 11 Dec 2021 07:35:47: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:35:47: #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 07:35:47: #1 tags after filtering in treatment: 5179892 INFO @ Sat, 11 Dec 2021 07:35:47: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 11 Dec 2021 07:35:47: #1 finished! INFO @ Sat, 11 Dec 2021 07:35:47: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:35:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:35:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9372360/SRX9372360.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9372360/SRX9372360.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9372360/SRX9372360.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9372360/SRX9372360.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 07:35:47: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:35:47: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:35:47: #2 number of paired peaks: 176 WARNING @ Sat, 11 Dec 2021 07:35:47: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 11 Dec 2021 07:35:47: start model_add_line... INFO @ Sat, 11 Dec 2021 07:35:47: start X-correlation... INFO @ Sat, 11 Dec 2021 07:35:47: end of X-cor INFO @ Sat, 11 Dec 2021 07:35:47: #2 finished! INFO @ Sat, 11 Dec 2021 07:35:47: #2 predicted fragment length is 151 bps INFO @ Sat, 11 Dec 2021 07:35:47: #2 alternative fragment length(s) may be 151 bps INFO @ Sat, 11 Dec 2021 07:35:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9372360/SRX9372360.05_model.r INFO @ Sat, 11 Dec 2021 07:35:47: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:35:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:35:49: 6000000 INFO @ Sat, 11 Dec 2021 07:35:53: 1000000 INFO @ Sat, 11 Dec 2021 07:35:54: 7000000 INFO @ Sat, 11 Dec 2021 07:35:58: 2000000 INFO @ Sat, 11 Dec 2021 07:35:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:35:59: 8000000 INFO @ Sat, 11 Dec 2021 07:36:04: 3000000 INFO @ Sat, 11 Dec 2021 07:36:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9372360/SRX9372360.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:36:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9372360/SRX9372360.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:36:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9372360/SRX9372360.05_summits.bed INFO @ Sat, 11 Dec 2021 07:36:04: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (604 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:36:04: 9000000 INFO @ Sat, 11 Dec 2021 07:36:09: 4000000 INFO @ Sat, 11 Dec 2021 07:36:09: 10000000 INFO @ Sat, 11 Dec 2021 07:36:15: 11000000 INFO @ Sat, 11 Dec 2021 07:36:15: 5000000 INFO @ Sat, 11 Dec 2021 07:36:19: #1 tag size is determined as 43 bps INFO @ Sat, 11 Dec 2021 07:36:19: #1 tag size = 43 INFO @ Sat, 11 Dec 2021 07:36:19: #1 total tags in treatment: 5292100 INFO @ Sat, 11 Dec 2021 07:36:19: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:36:19: #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 07:36:19: #1 tags after filtering in treatment: 5179892 INFO @ Sat, 11 Dec 2021 07:36:19: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 11 Dec 2021 07:36:19: #1 finished! INFO @ Sat, 11 Dec 2021 07:36:19: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:36:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:36:19: #2 number of paired peaks: 176 WARNING @ Sat, 11 Dec 2021 07:36:19: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 11 Dec 2021 07:36:19: start model_add_line... INFO @ Sat, 11 Dec 2021 07:36:19: start X-correlation... INFO @ Sat, 11 Dec 2021 07:36:19: end of X-cor INFO @ Sat, 11 Dec 2021 07:36:19: #2 finished! INFO @ Sat, 11 Dec 2021 07:36:19: #2 predicted fragment length is 151 bps INFO @ Sat, 11 Dec 2021 07:36:19: #2 alternative fragment length(s) may be 151 bps INFO @ Sat, 11 Dec 2021 07:36:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9372360/SRX9372360.10_model.r INFO @ Sat, 11 Dec 2021 07:36:19: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:36:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:36:20: 6000000 INFO @ Sat, 11 Dec 2021 07:36:25: 7000000 INFO @ Sat, 11 Dec 2021 07:36:30: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:36:31: 8000000 INFO @ Sat, 11 Dec 2021 07:36:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9372360/SRX9372360.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:36:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9372360/SRX9372360.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:36:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9372360/SRX9372360.10_summits.bed INFO @ Sat, 11 Dec 2021 07:36:36: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (431 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:36:36: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:36:41: 10000000 INFO @ Sat, 11 Dec 2021 07:36:46: 11000000 INFO @ Sat, 11 Dec 2021 07:36:51: #1 tag size is determined as 43 bps INFO @ Sat, 11 Dec 2021 07:36:51: #1 tag size = 43 INFO @ Sat, 11 Dec 2021 07:36:51: #1 total tags in treatment: 5292100 INFO @ Sat, 11 Dec 2021 07:36:51: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:36:51: #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 07:36:51: #1 tags after filtering in treatment: 5179892 INFO @ Sat, 11 Dec 2021 07:36:51: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 11 Dec 2021 07:36:51: #1 finished! INFO @ Sat, 11 Dec 2021 07:36:51: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:36:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:36:51: #2 number of paired peaks: 176 WARNING @ Sat, 11 Dec 2021 07:36:51: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 11 Dec 2021 07:36:51: start model_add_line... INFO @ Sat, 11 Dec 2021 07:36:51: start X-correlation... INFO @ Sat, 11 Dec 2021 07:36:51: end of X-cor INFO @ Sat, 11 Dec 2021 07:36:51: #2 finished! INFO @ Sat, 11 Dec 2021 07:36:51: #2 predicted fragment length is 151 bps INFO @ Sat, 11 Dec 2021 07:36:51: #2 alternative fragment length(s) may be 151 bps INFO @ Sat, 11 Dec 2021 07:36:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9372360/SRX9372360.20_model.r INFO @ Sat, 11 Dec 2021 07:36:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:36:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:37:02: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:37:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9372360/SRX9372360.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:37:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9372360/SRX9372360.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:37:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9372360/SRX9372360.20_summits.bed INFO @ Sat, 11 Dec 2021 07:37:08: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (248 records, 4 fields): 1 millis CompletedMACS2peakCalling