Job ID = 6529586 SRX = SRX331370 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:27 21559305 reads; of these: 21559305 (100.00%) were unpaired; of these: 1516199 (7.03%) aligned 0 times 15525225 (72.01%) aligned exactly 1 time 4517881 (20.96%) aligned >1 times 92.97% overall alignment rate Time searching: 00:06:27 Overall time: 00:06:27 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 2294965 / 20043106 = 0.1145 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:26:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331370/SRX331370.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331370/SRX331370.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331370/SRX331370.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331370/SRX331370.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 @ Tue, 30 Jun 2020 02:26:58: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:26:58: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:27:04: 1000000 INFO @ Tue, 30 Jun 2020 02:27:09: 2000000 INFO @ Tue, 30 Jun 2020 02:27:15: 3000000 INFO @ Tue, 30 Jun 2020 02:27:21: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:27:27: 5000000 INFO @ Tue, 30 Jun 2020 02:27:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331370/SRX331370.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331370/SRX331370.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331370/SRX331370.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331370/SRX331370.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 @ Tue, 30 Jun 2020 02:27:28: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:27:28: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:27:32: 6000000 INFO @ Tue, 30 Jun 2020 02:27:33: 1000000 INFO @ Tue, 30 Jun 2020 02:27:38: 7000000 INFO @ Tue, 30 Jun 2020 02:27:39: 2000000 INFO @ Tue, 30 Jun 2020 02:27:43: 8000000 INFO @ Tue, 30 Jun 2020 02:27:44: 3000000 INFO @ Tue, 30 Jun 2020 02:27:49: 9000000 INFO @ Tue, 30 Jun 2020 02:27:50: 4000000 INFO @ Tue, 30 Jun 2020 02:27:54: 10000000 INFO @ Tue, 30 Jun 2020 02:27:55: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:27:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331370/SRX331370.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331370/SRX331370.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331370/SRX331370.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331370/SRX331370.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 @ Tue, 30 Jun 2020 02:27:58: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:27:58: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:28:00: 11000000 INFO @ Tue, 30 Jun 2020 02:28:01: 6000000 INFO @ Tue, 30 Jun 2020 02:28:04: 1000000 INFO @ Tue, 30 Jun 2020 02:28:05: 12000000 INFO @ Tue, 30 Jun 2020 02:28:06: 7000000 INFO @ Tue, 30 Jun 2020 02:28:09: 2000000 INFO @ Tue, 30 Jun 2020 02:28:11: 13000000 INFO @ Tue, 30 Jun 2020 02:28:12: 8000000 INFO @ Tue, 30 Jun 2020 02:28:15: 3000000 INFO @ Tue, 30 Jun 2020 02:28:16: 14000000 INFO @ Tue, 30 Jun 2020 02:28:17: 9000000 INFO @ Tue, 30 Jun 2020 02:28:21: 4000000 INFO @ Tue, 30 Jun 2020 02:28:22: 10000000 INFO @ Tue, 30 Jun 2020 02:28:23: 15000000 INFO @ Tue, 30 Jun 2020 02:28:27: 5000000 INFO @ Tue, 30 Jun 2020 02:28:28: 11000000 INFO @ Tue, 30 Jun 2020 02:28:28: 16000000 INFO @ Tue, 30 Jun 2020 02:28:33: 6000000 INFO @ Tue, 30 Jun 2020 02:28:34: 12000000 INFO @ Tue, 30 Jun 2020 02:28:34: 17000000 INFO @ Tue, 30 Jun 2020 02:28:38: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:28:38: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:28:38: #1 total tags in treatment: 17748141 INFO @ Tue, 30 Jun 2020 02:28:38: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:28:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:28:39: 7000000 INFO @ Tue, 30 Jun 2020 02:28:39: 13000000 INFO @ Tue, 30 Jun 2020 02:28:39: #1 tags after filtering in treatment: 17748141 INFO @ Tue, 30 Jun 2020 02:28:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:28:39: #1 finished! INFO @ Tue, 30 Jun 2020 02:28:39: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:28:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:28:40: #2 number of paired peaks: 245 WARNING @ Tue, 30 Jun 2020 02:28:40: Fewer paired peaks (245) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 245 pairs to build model! INFO @ Tue, 30 Jun 2020 02:28:40: start model_add_line... INFO @ Tue, 30 Jun 2020 02:28:41: start X-correlation... INFO @ Tue, 30 Jun 2020 02:28:41: end of X-cor INFO @ Tue, 30 Jun 2020 02:28:41: #2 finished! INFO @ Tue, 30 Jun 2020 02:28:41: #2 predicted fragment length is 3 bps INFO @ Tue, 30 Jun 2020 02:28:41: #2 alternative fragment length(s) may be 3,19,36 bps INFO @ Tue, 30 Jun 2020 02:28:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331370/SRX331370.05_model.r WARNING @ Tue, 30 Jun 2020 02:28:41: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:28:41: #2 You may need to consider one of the other alternative d(s): 3,19,36 WARNING @ Tue, 30 Jun 2020 02:28:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:28:41: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:28:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:28:44: 8000000 INFO @ Tue, 30 Jun 2020 02:28:45: 14000000 INFO @ Tue, 30 Jun 2020 02:28:50: 9000000 INFO @ Tue, 30 Jun 2020 02:28:51: 15000000 INFO @ Tue, 30 Jun 2020 02:28:56: 10000000 INFO @ Tue, 30 Jun 2020 02:28:56: 16000000 INFO @ Tue, 30 Jun 2020 02:29:01: 11000000 INFO @ Tue, 30 Jun 2020 02:29:02: 17000000 INFO @ Tue, 30 Jun 2020 02:29:06: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:29:06: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:29:06: #1 total tags in treatment: 17748141 INFO @ Tue, 30 Jun 2020 02:29:06: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:29:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:29:07: #1 tags after filtering in treatment: 17748141 INFO @ Tue, 30 Jun 2020 02:29:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:29:07: #1 finished! INFO @ Tue, 30 Jun 2020 02:29:07: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:29:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:29:07: 12000000 INFO @ Tue, 30 Jun 2020 02:29:08: #2 number of paired peaks: 245 WARNING @ Tue, 30 Jun 2020 02:29:08: Fewer paired peaks (245) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 245 pairs to build model! INFO @ Tue, 30 Jun 2020 02:29:08: start model_add_line... INFO @ Tue, 30 Jun 2020 02:29:08: start X-correlation... INFO @ Tue, 30 Jun 2020 02:29:08: end of X-cor INFO @ Tue, 30 Jun 2020 02:29:08: #2 finished! INFO @ Tue, 30 Jun 2020 02:29:08: #2 predicted fragment length is 3 bps INFO @ Tue, 30 Jun 2020 02:29:08: #2 alternative fragment length(s) may be 3,19,36 bps INFO @ Tue, 30 Jun 2020 02:29:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331370/SRX331370.10_model.r WARNING @ Tue, 30 Jun 2020 02:29:08: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:29:08: #2 You may need to consider one of the other alternative d(s): 3,19,36 WARNING @ Tue, 30 Jun 2020 02:29:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:29:08: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:29:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:29:13: 13000000 INFO @ Tue, 30 Jun 2020 02:29:17: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:29:19: 14000000 INFO @ Tue, 30 Jun 2020 02:29:25: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:29:31: 16000000 INFO @ Tue, 30 Jun 2020 02:29:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331370/SRX331370.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:29:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331370/SRX331370.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:29:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331370/SRX331370.05_summits.bed INFO @ Tue, 30 Jun 2020 02:29:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:29:36: 17000000 INFO @ Tue, 30 Jun 2020 02:29:41: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:29:41: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:29:41: #1 total tags in treatment: 17748141 INFO @ Tue, 30 Jun 2020 02:29:41: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:29:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:29:42: #1 tags after filtering in treatment: 17748141 INFO @ Tue, 30 Jun 2020 02:29:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:29:42: #1 finished! INFO @ Tue, 30 Jun 2020 02:29:42: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:29:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:29:43: #2 number of paired peaks: 245 WARNING @ Tue, 30 Jun 2020 02:29:43: Fewer paired peaks (245) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 245 pairs to build model! INFO @ Tue, 30 Jun 2020 02:29:43: start model_add_line... INFO @ Tue, 30 Jun 2020 02:29:43: start X-correlation... INFO @ Tue, 30 Jun 2020 02:29:43: end of X-cor INFO @ Tue, 30 Jun 2020 02:29:43: #2 finished! INFO @ Tue, 30 Jun 2020 02:29:43: #2 predicted fragment length is 3 bps INFO @ Tue, 30 Jun 2020 02:29:43: #2 alternative fragment length(s) may be 3,19,36 bps INFO @ Tue, 30 Jun 2020 02:29:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331370/SRX331370.20_model.r WARNING @ Tue, 30 Jun 2020 02:29:43: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:29:43: #2 You may need to consider one of the other alternative d(s): 3,19,36 WARNING @ Tue, 30 Jun 2020 02:29:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:29:43: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:29:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:29:44: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:30:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331370/SRX331370.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:30:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331370/SRX331370.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:30:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331370/SRX331370.10_summits.bed INFO @ Tue, 30 Jun 2020 02:30:01: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:30:19: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:30:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331370/SRX331370.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:30:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331370/SRX331370.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:30:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331370/SRX331370.20_summits.bed INFO @ Tue, 30 Jun 2020 02:30:36: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling