Job ID = 14171310 SRX = SRX9986142 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 24384523 spots for SRR13591505/SRR13591505.sra Written 24384523 spots for SRR13591505/SRR13591505.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171772 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:08:34 24384523 reads; of these: 24384523 (100.00%) were unpaired; of these: 1023321 (4.20%) aligned 0 times 14491972 (59.43%) aligned exactly 1 time 8869230 (36.37%) aligned >1 times 95.80% overall alignment rate Time searching: 00:08:35 Overall time: 00:08:35 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] 4534832 / 23361202 = 0.1941 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 11:22:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986142/SRX9986142.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986142/SRX9986142.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986142/SRX9986142.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986142/SRX9986142.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 11:22:15: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:22:15: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:22:20: 1000000 INFO @ Sat, 11 Dec 2021 11:22:25: 2000000 INFO @ Sat, 11 Dec 2021 11:22:30: 3000000 INFO @ Sat, 11 Dec 2021 11:22:35: 4000000 INFO @ Sat, 11 Dec 2021 11:22:40: 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 11:22:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986142/SRX9986142.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986142/SRX9986142.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986142/SRX9986142.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986142/SRX9986142.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 11:22:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:22:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:22:45: 6000000 INFO @ Sat, 11 Dec 2021 11:22:50: 1000000 INFO @ Sat, 11 Dec 2021 11:22:51: 7000000 INFO @ Sat, 11 Dec 2021 11:22:56: 2000000 INFO @ Sat, 11 Dec 2021 11:22:56: 8000000 INFO @ Sat, 11 Dec 2021 11:23:01: 3000000 INFO @ Sat, 11 Dec 2021 11:23:02: 9000000 INFO @ Sat, 11 Dec 2021 11:23:07: 4000000 INFO @ Sat, 11 Dec 2021 11:23:07: 10000000 INFO @ Sat, 11 Dec 2021 11:23:12: 5000000 INFO @ Sat, 11 Dec 2021 11:23:13: 11000000 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 11:23:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986142/SRX9986142.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986142/SRX9986142.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986142/SRX9986142.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986142/SRX9986142.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 11:23:15: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:23:15: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:23:18: 6000000 INFO @ Sat, 11 Dec 2021 11:23:18: 12000000 INFO @ Sat, 11 Dec 2021 11:23:20: 1000000 INFO @ Sat, 11 Dec 2021 11:23:23: 7000000 INFO @ Sat, 11 Dec 2021 11:23:24: 13000000 INFO @ Sat, 11 Dec 2021 11:23:26: 2000000 INFO @ Sat, 11 Dec 2021 11:23:29: 8000000 INFO @ Sat, 11 Dec 2021 11:23:29: 14000000 INFO @ Sat, 11 Dec 2021 11:23:31: 3000000 INFO @ Sat, 11 Dec 2021 11:23:34: 9000000 INFO @ Sat, 11 Dec 2021 11:23:35: 15000000 INFO @ Sat, 11 Dec 2021 11:23:37: 4000000 INFO @ Sat, 11 Dec 2021 11:23:40: 10000000 INFO @ Sat, 11 Dec 2021 11:23:41: 16000000 INFO @ Sat, 11 Dec 2021 11:23:43: 5000000 INFO @ Sat, 11 Dec 2021 11:23:45: 11000000 INFO @ Sat, 11 Dec 2021 11:23:46: 17000000 INFO @ Sat, 11 Dec 2021 11:23:48: 6000000 INFO @ Sat, 11 Dec 2021 11:23:51: 12000000 INFO @ Sat, 11 Dec 2021 11:23:52: 18000000 INFO @ Sat, 11 Dec 2021 11:23:54: 7000000 INFO @ Sat, 11 Dec 2021 11:23:56: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:23:56: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:23:56: #1 total tags in treatment: 18826370 INFO @ Sat, 11 Dec 2021 11:23:56: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:23:56: #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 11:23:57: 13000000 INFO @ Sat, 11 Dec 2021 11:23:57: #1 tags after filtering in treatment: 18826370 INFO @ Sat, 11 Dec 2021 11:23:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:23:57: #1 finished! INFO @ Sat, 11 Dec 2021 11:23:57: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:23:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:23:58: #2 number of paired peaks: 257 WARNING @ Sat, 11 Dec 2021 11:23:58: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Sat, 11 Dec 2021 11:23:58: start model_add_line... INFO @ Sat, 11 Dec 2021 11:23:58: start X-correlation... INFO @ Sat, 11 Dec 2021 11:23:58: end of X-cor INFO @ Sat, 11 Dec 2021 11:23:58: #2 finished! INFO @ Sat, 11 Dec 2021 11:23:58: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Dec 2021 11:23:58: #2 alternative fragment length(s) may be 3,49,503,545 bps INFO @ Sat, 11 Dec 2021 11:23:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986142/SRX9986142.05_model.r WARNING @ Sat, 11 Dec 2021 11:23:58: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:23:58: #2 You may need to consider one of the other alternative d(s): 3,49,503,545 WARNING @ Sat, 11 Dec 2021 11:23:58: #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 11:23:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:23:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:23:59: 8000000 INFO @ Sat, 11 Dec 2021 11:24:02: 14000000 INFO @ Sat, 11 Dec 2021 11:24:05: 9000000 INFO @ Sat, 11 Dec 2021 11:24:08: 15000000 INFO @ Sat, 11 Dec 2021 11:24:10: 10000000 INFO @ Sat, 11 Dec 2021 11:24:13: 16000000 INFO @ Sat, 11 Dec 2021 11:24:16: 11000000 INFO @ Sat, 11 Dec 2021 11:24:19: 17000000 INFO @ Sat, 11 Dec 2021 11:24:21: 12000000 INFO @ Sat, 11 Dec 2021 11:24:25: 18000000 INFO @ Sat, 11 Dec 2021 11:24:27: 13000000 INFO @ Sat, 11 Dec 2021 11:24:29: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:24:29: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:24:29: #1 total tags in treatment: 18826370 INFO @ Sat, 11 Dec 2021 11:24:29: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:24:29: #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 11:24:30: #1 tags after filtering in treatment: 18826370 INFO @ Sat, 11 Dec 2021 11:24:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:24:30: #1 finished! INFO @ Sat, 11 Dec 2021 11:24:30: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:24:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:24:31: #2 number of paired peaks: 257 WARNING @ Sat, 11 Dec 2021 11:24:31: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Sat, 11 Dec 2021 11:24:31: start model_add_line... INFO @ Sat, 11 Dec 2021 11:24:31: start X-correlation... INFO @ Sat, 11 Dec 2021 11:24:31: end of X-cor INFO @ Sat, 11 Dec 2021 11:24:31: #2 finished! INFO @ Sat, 11 Dec 2021 11:24:31: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Dec 2021 11:24:31: #2 alternative fragment length(s) may be 3,49,503,545 bps INFO @ Sat, 11 Dec 2021 11:24:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986142/SRX9986142.10_model.r WARNING @ Sat, 11 Dec 2021 11:24:31: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:24:31: #2 You may need to consider one of the other alternative d(s): 3,49,503,545 WARNING @ Sat, 11 Dec 2021 11:24:31: #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 11:24:31: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:24:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:24:32: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:24:32: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:24:38: 15000000 INFO @ Sat, 11 Dec 2021 11:24:43: 16000000 INFO @ Sat, 11 Dec 2021 11:24:48: 17000000 INFO @ Sat, 11 Dec 2021 11:24:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986142/SRX9986142.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:24:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986142/SRX9986142.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:24:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986142/SRX9986142.05_summits.bed INFO @ Sat, 11 Dec 2021 11:24:48: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3147 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:24:53: 18000000 INFO @ Sat, 11 Dec 2021 11:24:57: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:24:57: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:24:57: #1 total tags in treatment: 18826370 INFO @ Sat, 11 Dec 2021 11:24:57: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:24:57: #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 11:24:58: #1 tags after filtering in treatment: 18826370 INFO @ Sat, 11 Dec 2021 11:24:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:24:58: #1 finished! INFO @ Sat, 11 Dec 2021 11:24:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:24:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:24:59: #2 number of paired peaks: 257 WARNING @ Sat, 11 Dec 2021 11:24:59: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Sat, 11 Dec 2021 11:24:59: start model_add_line... INFO @ Sat, 11 Dec 2021 11:24:59: start X-correlation... INFO @ Sat, 11 Dec 2021 11:24:59: end of X-cor INFO @ Sat, 11 Dec 2021 11:24:59: #2 finished! INFO @ Sat, 11 Dec 2021 11:24:59: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Dec 2021 11:24:59: #2 alternative fragment length(s) may be 3,49,503,545 bps INFO @ Sat, 11 Dec 2021 11:24:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986142/SRX9986142.20_model.r WARNING @ Sat, 11 Dec 2021 11:24:59: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:24:59: #2 You may need to consider one of the other alternative d(s): 3,49,503,545 WARNING @ Sat, 11 Dec 2021 11:24:59: #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 11:24:59: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:24:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:25:05: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:25:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986142/SRX9986142.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:25:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986142/SRX9986142.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:25:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986142/SRX9986142.10_summits.bed INFO @ Sat, 11 Dec 2021 11:25:22: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2091 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:25:32: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:25:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986142/SRX9986142.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:25:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986142/SRX9986142.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:25:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986142/SRX9986142.20_summits.bed INFO @ Sat, 11 Dec 2021 11:25:49: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (948 records, 4 fields): 4 millis CompletedMACS2peakCalling