Job ID = 14172284 SRX = SRX3293000 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 29800365 spots for SRR6182826/SRR6182826.sra Written 29800365 spots for SRR6182826/SRR6182826.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172820 ("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: 00:14:09 29800365 reads; of these: 29800365 (100.00%) were unpaired; of these: 867951 (2.91%) aligned 0 times 23820354 (79.93%) aligned exactly 1 time 5112060 (17.15%) aligned >1 times 97.09% overall alignment rate Time searching: 00:14:09 Overall time: 00:14:09 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 12 files... [bam_rmdupse_core] 2555539 / 28932414 = 0.0883 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 15:28:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3293000/SRX3293000.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3293000/SRX3293000.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3293000/SRX3293000.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3293000/SRX3293000.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 15:28:07: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:28:07: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:28:13: 1000000 INFO @ Sat, 11 Dec 2021 15:28:18: 2000000 INFO @ Sat, 11 Dec 2021 15:28:24: 3000000 INFO @ Sat, 11 Dec 2021 15:28:30: 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 @ Sat, 11 Dec 2021 15:28:36: 5000000 INFO @ Sat, 11 Dec 2021 15:28:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3293000/SRX3293000.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3293000/SRX3293000.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3293000/SRX3293000.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3293000/SRX3293000.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 15:28:37: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:28:37: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:28:42: 6000000 INFO @ Sat, 11 Dec 2021 15:28:43: 1000000 INFO @ Sat, 11 Dec 2021 15:28:48: 7000000 INFO @ Sat, 11 Dec 2021 15:28:49: 2000000 INFO @ Sat, 11 Dec 2021 15:28:54: 8000000 INFO @ Sat, 11 Dec 2021 15:28:55: 3000000 INFO @ Sat, 11 Dec 2021 15:29:00: 9000000 INFO @ Sat, 11 Dec 2021 15:29:01: 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 15:29:06: 10000000 INFO @ Sat, 11 Dec 2021 15:29:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3293000/SRX3293000.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3293000/SRX3293000.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3293000/SRX3293000.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3293000/SRX3293000.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 15:29:07: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:29:07: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:29:07: 5000000 INFO @ Sat, 11 Dec 2021 15:29:12: 11000000 INFO @ Sat, 11 Dec 2021 15:29:13: 6000000 INFO @ Sat, 11 Dec 2021 15:29:13: 1000000 INFO @ Sat, 11 Dec 2021 15:29:18: 12000000 INFO @ Sat, 11 Dec 2021 15:29:19: 7000000 INFO @ Sat, 11 Dec 2021 15:29:19: 2000000 INFO @ Sat, 11 Dec 2021 15:29:24: 13000000 INFO @ Sat, 11 Dec 2021 15:29:25: 8000000 INFO @ Sat, 11 Dec 2021 15:29:25: 3000000 INFO @ Sat, 11 Dec 2021 15:29:29: 14000000 INFO @ Sat, 11 Dec 2021 15:29:31: 9000000 INFO @ Sat, 11 Dec 2021 15:29:31: 4000000 INFO @ Sat, 11 Dec 2021 15:29:35: 15000000 INFO @ Sat, 11 Dec 2021 15:29:37: 5000000 INFO @ Sat, 11 Dec 2021 15:29:37: 10000000 INFO @ Sat, 11 Dec 2021 15:29:41: 16000000 INFO @ Sat, 11 Dec 2021 15:29:43: 6000000 INFO @ Sat, 11 Dec 2021 15:29:43: 11000000 INFO @ Sat, 11 Dec 2021 15:29:47: 17000000 INFO @ Sat, 11 Dec 2021 15:29:49: 12000000 INFO @ Sat, 11 Dec 2021 15:29:49: 7000000 INFO @ Sat, 11 Dec 2021 15:29:53: 18000000 INFO @ Sat, 11 Dec 2021 15:29:55: 13000000 INFO @ Sat, 11 Dec 2021 15:29:55: 8000000 INFO @ Sat, 11 Dec 2021 15:29:59: 19000000 INFO @ Sat, 11 Dec 2021 15:30:01: 14000000 INFO @ Sat, 11 Dec 2021 15:30:01: 9000000 INFO @ Sat, 11 Dec 2021 15:30:05: 20000000 INFO @ Sat, 11 Dec 2021 15:30:07: 15000000 INFO @ Sat, 11 Dec 2021 15:30:07: 10000000 INFO @ Sat, 11 Dec 2021 15:30:11: 21000000 INFO @ Sat, 11 Dec 2021 15:30:13: 16000000 INFO @ Sat, 11 Dec 2021 15:30:13: 11000000 INFO @ Sat, 11 Dec 2021 15:30:17: 22000000 INFO @ Sat, 11 Dec 2021 15:30:19: 17000000 INFO @ Sat, 11 Dec 2021 15:30:19: 12000000 INFO @ Sat, 11 Dec 2021 15:30:23: 23000000 INFO @ Sat, 11 Dec 2021 15:30:25: 18000000 INFO @ Sat, 11 Dec 2021 15:30:25: 13000000 INFO @ Sat, 11 Dec 2021 15:30:29: 24000000 INFO @ Sat, 11 Dec 2021 15:30:31: 19000000 INFO @ Sat, 11 Dec 2021 15:30:31: 14000000 INFO @ Sat, 11 Dec 2021 15:30:34: 25000000 INFO @ Sat, 11 Dec 2021 15:30:37: 20000000 INFO @ Sat, 11 Dec 2021 15:30:37: 15000000 INFO @ Sat, 11 Dec 2021 15:30:40: 26000000 INFO @ Sat, 11 Dec 2021 15:30:43: 21000000 INFO @ Sat, 11 Dec 2021 15:30:43: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 15:30:43: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 15:30:43: #1 total tags in treatment: 26376875 INFO @ Sat, 11 Dec 2021 15:30:43: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:30:43: #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 15:30:43: 16000000 INFO @ Sat, 11 Dec 2021 15:30:43: #1 tags after filtering in treatment: 26376875 INFO @ Sat, 11 Dec 2021 15:30:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:30:43: #1 finished! INFO @ Sat, 11 Dec 2021 15:30:43: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:30:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:30:45: #2 number of paired peaks: 117 WARNING @ Sat, 11 Dec 2021 15:30:45: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Sat, 11 Dec 2021 15:30:45: start model_add_line... INFO @ Sat, 11 Dec 2021 15:30:45: start X-correlation... INFO @ Sat, 11 Dec 2021 15:30:45: end of X-cor INFO @ Sat, 11 Dec 2021 15:30:45: #2 finished! INFO @ Sat, 11 Dec 2021 15:30:45: #2 predicted fragment length is 104 bps INFO @ Sat, 11 Dec 2021 15:30:45: #2 alternative fragment length(s) may be 1,104,475,522,543,570 bps INFO @ Sat, 11 Dec 2021 15:30:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3293000/SRX3293000.05_model.r WARNING @ Sat, 11 Dec 2021 15:30:45: #2 Since the d (104) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:30:45: #2 You may need to consider one of the other alternative d(s): 1,104,475,522,543,570 WARNING @ Sat, 11 Dec 2021 15:30:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 15:30:45: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:30:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:30:48: 22000000 INFO @ Sat, 11 Dec 2021 15:30:49: 17000000 INFO @ Sat, 11 Dec 2021 15:30:54: 23000000 INFO @ Sat, 11 Dec 2021 15:30:55: 18000000 INFO @ Sat, 11 Dec 2021 15:31:00: 24000000 INFO @ Sat, 11 Dec 2021 15:31:01: 19000000 INFO @ Sat, 11 Dec 2021 15:31:06: 25000000 INFO @ Sat, 11 Dec 2021 15:31:07: 20000000 INFO @ Sat, 11 Dec 2021 15:31:12: 26000000 INFO @ Sat, 11 Dec 2021 15:31:12: 21000000 INFO @ Sat, 11 Dec 2021 15:31:15: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 15:31:15: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 15:31:15: #1 total tags in treatment: 26376875 INFO @ Sat, 11 Dec 2021 15:31:15: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:31:15: #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 15:31:15: #1 tags after filtering in treatment: 26376875 INFO @ Sat, 11 Dec 2021 15:31:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:31:15: #1 finished! INFO @ Sat, 11 Dec 2021 15:31:15: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:31:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:31:17: #2 number of paired peaks: 117 WARNING @ Sat, 11 Dec 2021 15:31:17: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Sat, 11 Dec 2021 15:31:17: start model_add_line... INFO @ Sat, 11 Dec 2021 15:31:17: start X-correlation... INFO @ Sat, 11 Dec 2021 15:31:17: end of X-cor INFO @ Sat, 11 Dec 2021 15:31:17: #2 finished! INFO @ Sat, 11 Dec 2021 15:31:17: #2 predicted fragment length is 104 bps INFO @ Sat, 11 Dec 2021 15:31:17: #2 alternative fragment length(s) may be 1,104,475,522,543,570 bps INFO @ Sat, 11 Dec 2021 15:31:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3293000/SRX3293000.10_model.r WARNING @ Sat, 11 Dec 2021 15:31:17: #2 Since the d (104) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:31:17: #2 You may need to consider one of the other alternative d(s): 1,104,475,522,543,570 WARNING @ Sat, 11 Dec 2021 15:31:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 15:31:17: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:31:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:31:18: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:31:24: 23000000 INFO @ Sat, 11 Dec 2021 15:31:27: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:31:30: 24000000 INFO @ Sat, 11 Dec 2021 15:31:36: 25000000 INFO @ Sat, 11 Dec 2021 15:31:42: 26000000 INFO @ Sat, 11 Dec 2021 15:31:44: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 15:31:44: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 15:31:44: #1 total tags in treatment: 26376875 INFO @ Sat, 11 Dec 2021 15:31:44: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:31:44: #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 15:31:45: #1 tags after filtering in treatment: 26376875 INFO @ Sat, 11 Dec 2021 15:31:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:31:45: #1 finished! INFO @ Sat, 11 Dec 2021 15:31:45: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:31:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:31:46: #2 number of paired peaks: 117 WARNING @ Sat, 11 Dec 2021 15:31:46: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Sat, 11 Dec 2021 15:31:46: start model_add_line... INFO @ Sat, 11 Dec 2021 15:31:46: start X-correlation... INFO @ Sat, 11 Dec 2021 15:31:46: end of X-cor INFO @ Sat, 11 Dec 2021 15:31:46: #2 finished! INFO @ Sat, 11 Dec 2021 15:31:46: #2 predicted fragment length is 104 bps INFO @ Sat, 11 Dec 2021 15:31:46: #2 alternative fragment length(s) may be 1,104,475,522,543,570 bps INFO @ Sat, 11 Dec 2021 15:31:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3293000/SRX3293000.20_model.r WARNING @ Sat, 11 Dec 2021 15:31:46: #2 Since the d (104) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:31:46: #2 You may need to consider one of the other alternative d(s): 1,104,475,522,543,570 WARNING @ Sat, 11 Dec 2021 15:31:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 15:31:46: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:31:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:31:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3293000/SRX3293000.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:31:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3293000/SRX3293000.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:31:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3293000/SRX3293000.05_summits.bed INFO @ Sat, 11 Dec 2021 15:31:49: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (891 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:32:00: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:32:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3293000/SRX3293000.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:32:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3293000/SRX3293000.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:32:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3293000/SRX3293000.10_summits.bed INFO @ Sat, 11 Dec 2021 15:32:22: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (520 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:32:28: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:32:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3293000/SRX3293000.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:32:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3293000/SRX3293000.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:32:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3293000/SRX3293000.20_summits.bed INFO @ Sat, 11 Dec 2021 15:32:50: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (219 records, 4 fields): 2 millis CompletedMACS2peakCalling