Job ID = 12265313 SRX = SRX5010772 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 47570852 spots for SRR8191197/SRR8191197.sra Written 47570852 spots for SRR8191197/SRR8191197.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265509 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:14:05 47570852 reads; of these: 47570852 (100.00%) were unpaired; of these: 2764971 (5.81%) aligned 0 times 23757544 (49.94%) aligned exactly 1 time 21048337 (44.25%) aligned >1 times 94.19% overall alignment rate Time searching: 00:14:06 Overall time: 00:14:06 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 20 files... [bam_rmdupse_core] 26624371 / 44805881 = 0.5942 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:58:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010772/SRX5010772.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010772/SRX5010772.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010772/SRX5010772.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010772/SRX5010772.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, 03 Apr 2021 06:58:05: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:58:05: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:58:10: 1000000 INFO @ Sat, 03 Apr 2021 06:58:15: 2000000 INFO @ Sat, 03 Apr 2021 06:58:20: 3000000 INFO @ Sat, 03 Apr 2021 06:58:25: 4000000 INFO @ Sat, 03 Apr 2021 06:58:30: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:58:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010772/SRX5010772.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010772/SRX5010772.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010772/SRX5010772.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010772/SRX5010772.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, 03 Apr 2021 06:58:35: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:58:35: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:58:35: 6000000 INFO @ Sat, 03 Apr 2021 06:58:41: 7000000 INFO @ Sat, 03 Apr 2021 06:58:41: 1000000 INFO @ Sat, 03 Apr 2021 06:58:46: 8000000 INFO @ Sat, 03 Apr 2021 06:58:47: 2000000 INFO @ Sat, 03 Apr 2021 06:58:51: 9000000 INFO @ Sat, 03 Apr 2021 06:58:53: 3000000 INFO @ Sat, 03 Apr 2021 06:58:56: 10000000 INFO @ Sat, 03 Apr 2021 06:58:58: 4000000 INFO @ Sat, 03 Apr 2021 06:59:01: 11000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:59:04: 5000000 INFO @ Sat, 03 Apr 2021 06:59:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010772/SRX5010772.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010772/SRX5010772.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010772/SRX5010772.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010772/SRX5010772.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, 03 Apr 2021 06:59:05: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:59:05: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:59:07: 12000000 INFO @ Sat, 03 Apr 2021 06:59:10: 6000000 INFO @ Sat, 03 Apr 2021 06:59:11: 1000000 INFO @ Sat, 03 Apr 2021 06:59:12: 13000000 INFO @ Sat, 03 Apr 2021 06:59:16: 7000000 INFO @ Sat, 03 Apr 2021 06:59:17: 2000000 INFO @ Sat, 03 Apr 2021 06:59:17: 14000000 INFO @ Sat, 03 Apr 2021 06:59:22: 8000000 INFO @ Sat, 03 Apr 2021 06:59:22: 15000000 INFO @ Sat, 03 Apr 2021 06:59:23: 3000000 INFO @ Sat, 03 Apr 2021 06:59:28: 16000000 INFO @ Sat, 03 Apr 2021 06:59:28: 9000000 INFO @ Sat, 03 Apr 2021 06:59:28: 4000000 INFO @ Sat, 03 Apr 2021 06:59:33: 17000000 INFO @ Sat, 03 Apr 2021 06:59:34: 5000000 INFO @ Sat, 03 Apr 2021 06:59:34: 10000000 INFO @ Sat, 03 Apr 2021 06:59:38: 18000000 INFO @ Sat, 03 Apr 2021 06:59:40: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:59:40: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:59:40: #1 total tags in treatment: 18181510 INFO @ Sat, 03 Apr 2021 06:59:40: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:59:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:59:40: #1 tags after filtering in treatment: 18181510 INFO @ Sat, 03 Apr 2021 06:59:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:59:40: #1 finished! INFO @ Sat, 03 Apr 2021 06:59:40: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:59:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:59:40: 6000000 INFO @ Sat, 03 Apr 2021 06:59:41: 11000000 INFO @ Sat, 03 Apr 2021 06:59:41: #2 number of paired peaks: 141 WARNING @ Sat, 03 Apr 2021 06:59:41: Fewer paired peaks (141) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 141 pairs to build model! INFO @ Sat, 03 Apr 2021 06:59:41: start model_add_line... INFO @ Sat, 03 Apr 2021 06:59:41: start X-correlation... INFO @ Sat, 03 Apr 2021 06:59:41: end of X-cor INFO @ Sat, 03 Apr 2021 06:59:41: #2 finished! INFO @ Sat, 03 Apr 2021 06:59:41: #2 predicted fragment length is 40 bps INFO @ Sat, 03 Apr 2021 06:59:41: #2 alternative fragment length(s) may be 3,40,527,550 bps INFO @ Sat, 03 Apr 2021 06:59:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010772/SRX5010772.05_model.r WARNING @ Sat, 03 Apr 2021 06:59:41: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:59:41: #2 You may need to consider one of the other alternative d(s): 3,40,527,550 WARNING @ Sat, 03 Apr 2021 06:59:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:59:41: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:59:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:59:46: 7000000 INFO @ Sat, 03 Apr 2021 06:59:47: 12000000 INFO @ Sat, 03 Apr 2021 06:59:52: 8000000 INFO @ Sat, 03 Apr 2021 06:59:53: 13000000 INFO @ Sat, 03 Apr 2021 06:59:58: 9000000 INFO @ Sat, 03 Apr 2021 06:59:59: 14000000 INFO @ Sat, 03 Apr 2021 07:00:04: 10000000 INFO @ Sat, 03 Apr 2021 07:00:05: 15000000 INFO @ Sat, 03 Apr 2021 07:00:10: 11000000 INFO @ Sat, 03 Apr 2021 07:00:11: 16000000 INFO @ Sat, 03 Apr 2021 07:00:16: 12000000 INFO @ Sat, 03 Apr 2021 07:00:17: 17000000 INFO @ Sat, 03 Apr 2021 07:00:21: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:00:22: 13000000 INFO @ Sat, 03 Apr 2021 07:00:23: 18000000 INFO @ Sat, 03 Apr 2021 07:00:24: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:00:24: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:00:24: #1 total tags in treatment: 18181510 INFO @ Sat, 03 Apr 2021 07:00:24: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:00:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:00:25: #1 tags after filtering in treatment: 18181510 INFO @ Sat, 03 Apr 2021 07:00:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:00:25: #1 finished! INFO @ Sat, 03 Apr 2021 07:00:25: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:00:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:00:26: #2 number of paired peaks: 141 WARNING @ Sat, 03 Apr 2021 07:00:26: Fewer paired peaks (141) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 141 pairs to build model! INFO @ Sat, 03 Apr 2021 07:00:26: start model_add_line... INFO @ Sat, 03 Apr 2021 07:00:26: start X-correlation... INFO @ Sat, 03 Apr 2021 07:00:26: end of X-cor INFO @ Sat, 03 Apr 2021 07:00:26: #2 finished! INFO @ Sat, 03 Apr 2021 07:00:26: #2 predicted fragment length is 40 bps INFO @ Sat, 03 Apr 2021 07:00:26: #2 alternative fragment length(s) may be 3,40,527,550 bps INFO @ Sat, 03 Apr 2021 07:00:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010772/SRX5010772.10_model.r WARNING @ Sat, 03 Apr 2021 07:00:26: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:00:26: #2 You may need to consider one of the other alternative d(s): 3,40,527,550 WARNING @ Sat, 03 Apr 2021 07:00:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:00:26: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:00:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:00:28: 14000000 INFO @ Sat, 03 Apr 2021 07:00:33: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:00:39: 16000000 INFO @ Sat, 03 Apr 2021 07:00:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010772/SRX5010772.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:00:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010772/SRX5010772.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:00:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010772/SRX5010772.05_summits.bed INFO @ Sat, 03 Apr 2021 07:00:42: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5168 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:00:45: 17000000 INFO @ Sat, 03 Apr 2021 07:00:51: 18000000 INFO @ Sat, 03 Apr 2021 07:00:52: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:00:52: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:00:52: #1 total tags in treatment: 18181510 INFO @ Sat, 03 Apr 2021 07:00:52: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:00:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:00:52: #1 tags after filtering in treatment: 18181510 INFO @ Sat, 03 Apr 2021 07:00:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:00:52: #1 finished! INFO @ Sat, 03 Apr 2021 07:00:52: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:00:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:00:54: #2 number of paired peaks: 141 WARNING @ Sat, 03 Apr 2021 07:00:54: Fewer paired peaks (141) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 141 pairs to build model! INFO @ Sat, 03 Apr 2021 07:00:54: start model_add_line... INFO @ Sat, 03 Apr 2021 07:00:54: start X-correlation... INFO @ Sat, 03 Apr 2021 07:00:54: end of X-cor INFO @ Sat, 03 Apr 2021 07:00:54: #2 finished! INFO @ Sat, 03 Apr 2021 07:00:54: #2 predicted fragment length is 40 bps INFO @ Sat, 03 Apr 2021 07:00:54: #2 alternative fragment length(s) may be 3,40,527,550 bps INFO @ Sat, 03 Apr 2021 07:00:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010772/SRX5010772.20_model.r WARNING @ Sat, 03 Apr 2021 07:00:54: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:00:54: #2 You may need to consider one of the other alternative d(s): 3,40,527,550 WARNING @ Sat, 03 Apr 2021 07:00:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:00:54: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:00:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:01:06: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:01:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010772/SRX5010772.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:01:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010772/SRX5010772.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:01:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010772/SRX5010772.10_summits.bed INFO @ Sat, 03 Apr 2021 07:01:25: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2114 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:01:34: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:01:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010772/SRX5010772.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:01:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010772/SRX5010772.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:01:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010772/SRX5010772.20_summits.bed INFO @ Sat, 03 Apr 2021 07:01:54: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (185 records, 4 fields): 1 millis CompletedMACS2peakCalling