Job ID = 6529669 SRX = SRX3981632 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: 00:10:08 41236933 reads; of these: 41236933 (100.00%) were unpaired; of these: 1307124 (3.17%) aligned 0 times 30008903 (72.77%) aligned exactly 1 time 9920906 (24.06%) aligned >1 times 96.83% overall alignment rate Time searching: 00:10:08 Overall time: 00:10:08 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 20 files... [bam_rmdupse_core] 5342058 / 39929809 = 0.1338 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 03:35:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981632/SRX3981632.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981632/SRX3981632.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981632/SRX3981632.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981632/SRX3981632.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 03:35:51: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:35:51: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:35:56: 1000000 INFO @ Tue, 30 Jun 2020 03:36:01: 2000000 INFO @ Tue, 30 Jun 2020 03:36:06: 3000000 INFO @ Tue, 30 Jun 2020 03:36:11: 4000000 INFO @ Tue, 30 Jun 2020 03:36:16: 5000000 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 03:36:21: 6000000 INFO @ Tue, 30 Jun 2020 03:36:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981632/SRX3981632.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981632/SRX3981632.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981632/SRX3981632.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981632/SRX3981632.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 03:36:21: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:36:21: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:36:26: 7000000 INFO @ Tue, 30 Jun 2020 03:36:26: 1000000 INFO @ Tue, 30 Jun 2020 03:36:32: 8000000 INFO @ Tue, 30 Jun 2020 03:36:32: 2000000 INFO @ Tue, 30 Jun 2020 03:36:37: 9000000 INFO @ Tue, 30 Jun 2020 03:36:37: 3000000 INFO @ Tue, 30 Jun 2020 03:36:42: 10000000 INFO @ Tue, 30 Jun 2020 03:36:42: 4000000 INFO @ Tue, 30 Jun 2020 03:36:48: 11000000 INFO @ Tue, 30 Jun 2020 03:36:48: 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 03:36:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981632/SRX3981632.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981632/SRX3981632.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981632/SRX3981632.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981632/SRX3981632.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 03:36:51: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:36:51: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:36:53: 12000000 INFO @ Tue, 30 Jun 2020 03:36:53: 6000000 INFO @ Tue, 30 Jun 2020 03:36:57: 1000000 INFO @ Tue, 30 Jun 2020 03:36:59: 13000000 INFO @ Tue, 30 Jun 2020 03:36:59: 7000000 INFO @ Tue, 30 Jun 2020 03:37:02: 2000000 INFO @ Tue, 30 Jun 2020 03:37:04: 14000000 INFO @ Tue, 30 Jun 2020 03:37:05: 8000000 INFO @ Tue, 30 Jun 2020 03:37:08: 3000000 INFO @ Tue, 30 Jun 2020 03:37:10: 15000000 INFO @ Tue, 30 Jun 2020 03:37:10: 9000000 INFO @ Tue, 30 Jun 2020 03:37:14: 4000000 INFO @ Tue, 30 Jun 2020 03:37:15: 16000000 INFO @ Tue, 30 Jun 2020 03:37:16: 10000000 INFO @ Tue, 30 Jun 2020 03:37:19: 5000000 INFO @ Tue, 30 Jun 2020 03:37:21: 17000000 INFO @ Tue, 30 Jun 2020 03:37:22: 11000000 INFO @ Tue, 30 Jun 2020 03:37:25: 6000000 INFO @ Tue, 30 Jun 2020 03:37:27: 18000000 INFO @ Tue, 30 Jun 2020 03:37:27: 12000000 INFO @ Tue, 30 Jun 2020 03:37:31: 7000000 INFO @ Tue, 30 Jun 2020 03:37:32: 19000000 INFO @ Tue, 30 Jun 2020 03:37:33: 13000000 INFO @ Tue, 30 Jun 2020 03:37:36: 8000000 INFO @ Tue, 30 Jun 2020 03:37:38: 20000000 INFO @ Tue, 30 Jun 2020 03:37:38: 14000000 INFO @ Tue, 30 Jun 2020 03:37:42: 9000000 INFO @ Tue, 30 Jun 2020 03:37:43: 21000000 INFO @ Tue, 30 Jun 2020 03:37:44: 15000000 INFO @ Tue, 30 Jun 2020 03:37:47: 10000000 INFO @ Tue, 30 Jun 2020 03:37:49: 22000000 INFO @ Tue, 30 Jun 2020 03:37:50: 16000000 INFO @ Tue, 30 Jun 2020 03:37:53: 11000000 INFO @ Tue, 30 Jun 2020 03:37:54: 23000000 INFO @ Tue, 30 Jun 2020 03:37:55: 17000000 INFO @ Tue, 30 Jun 2020 03:37:59: 12000000 INFO @ Tue, 30 Jun 2020 03:37:59: 24000000 INFO @ Tue, 30 Jun 2020 03:38:01: 18000000 INFO @ Tue, 30 Jun 2020 03:38:04: 13000000 INFO @ Tue, 30 Jun 2020 03:38:05: 25000000 INFO @ Tue, 30 Jun 2020 03:38:06: 19000000 INFO @ Tue, 30 Jun 2020 03:38:10: 14000000 INFO @ Tue, 30 Jun 2020 03:38:10: 26000000 INFO @ Tue, 30 Jun 2020 03:38:12: 20000000 INFO @ Tue, 30 Jun 2020 03:38:15: 15000000 INFO @ Tue, 30 Jun 2020 03:38:16: 27000000 INFO @ Tue, 30 Jun 2020 03:38:18: 21000000 INFO @ Tue, 30 Jun 2020 03:38:21: 16000000 INFO @ Tue, 30 Jun 2020 03:38:21: 28000000 INFO @ Tue, 30 Jun 2020 03:38:23: 22000000 INFO @ Tue, 30 Jun 2020 03:38:26: 17000000 INFO @ Tue, 30 Jun 2020 03:38:27: 29000000 INFO @ Tue, 30 Jun 2020 03:38:28: 23000000 INFO @ Tue, 30 Jun 2020 03:38:32: 18000000 INFO @ Tue, 30 Jun 2020 03:38:32: 30000000 INFO @ Tue, 30 Jun 2020 03:38:34: 24000000 INFO @ Tue, 30 Jun 2020 03:38:37: 19000000 INFO @ Tue, 30 Jun 2020 03:38:38: 31000000 INFO @ Tue, 30 Jun 2020 03:38:39: 25000000 INFO @ Tue, 30 Jun 2020 03:38:43: 20000000 INFO @ Tue, 30 Jun 2020 03:38:43: 32000000 INFO @ Tue, 30 Jun 2020 03:38:45: 26000000 INFO @ Tue, 30 Jun 2020 03:38:48: 21000000 INFO @ Tue, 30 Jun 2020 03:38:49: 33000000 INFO @ Tue, 30 Jun 2020 03:38:50: 27000000 INFO @ Tue, 30 Jun 2020 03:38:54: 22000000 INFO @ Tue, 30 Jun 2020 03:38:54: 34000000 INFO @ Tue, 30 Jun 2020 03:38:56: 28000000 INFO @ Tue, 30 Jun 2020 03:38:58: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:38:58: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:38:58: #1 total tags in treatment: 34587751 INFO @ Tue, 30 Jun 2020 03:38:58: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:38:58: #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 03:38:58: #1 tags after filtering in treatment: 34587710 INFO @ Tue, 30 Jun 2020 03:38:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:38:58: #1 finished! INFO @ Tue, 30 Jun 2020 03:38:58: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:38:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:38:59: 23000000 INFO @ Tue, 30 Jun 2020 03:39:00: #2 number of paired peaks: 146 WARNING @ Tue, 30 Jun 2020 03:39:00: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Tue, 30 Jun 2020 03:39:00: start model_add_line... INFO @ Tue, 30 Jun 2020 03:39:01: start X-correlation... INFO @ Tue, 30 Jun 2020 03:39:01: end of X-cor INFO @ Tue, 30 Jun 2020 03:39:01: #2 finished! INFO @ Tue, 30 Jun 2020 03:39:01: #2 predicted fragment length is 41 bps INFO @ Tue, 30 Jun 2020 03:39:01: #2 alternative fragment length(s) may be 2,41,158,445,573,591 bps INFO @ Tue, 30 Jun 2020 03:39:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981632/SRX3981632.05_model.r WARNING @ Tue, 30 Jun 2020 03:39:01: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:39:01: #2 You may need to consider one of the other alternative d(s): 2,41,158,445,573,591 WARNING @ Tue, 30 Jun 2020 03:39:01: #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 03:39:01: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:39:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:39:01: 29000000 INFO @ Tue, 30 Jun 2020 03:39:04: 24000000 INFO @ Tue, 30 Jun 2020 03:39:07: 30000000 INFO @ Tue, 30 Jun 2020 03:39:10: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:39:12: 31000000 INFO @ Tue, 30 Jun 2020 03:39:15: 26000000 INFO @ Tue, 30 Jun 2020 03:39:17: 32000000 INFO @ Tue, 30 Jun 2020 03:39:21: 27000000 INFO @ Tue, 30 Jun 2020 03:39:23: 33000000 INFO @ Tue, 30 Jun 2020 03:39:26: 28000000 INFO @ Tue, 30 Jun 2020 03:39:28: 34000000 INFO @ Tue, 30 Jun 2020 03:39:31: 29000000 INFO @ Tue, 30 Jun 2020 03:39:32: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:39:32: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:39:32: #1 total tags in treatment: 34587751 INFO @ Tue, 30 Jun 2020 03:39:32: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:39:32: #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 03:39:32: #1 tags after filtering in treatment: 34587710 INFO @ Tue, 30 Jun 2020 03:39:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:39:32: #1 finished! INFO @ Tue, 30 Jun 2020 03:39:32: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:39:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:39:35: #2 number of paired peaks: 146 WARNING @ Tue, 30 Jun 2020 03:39:35: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Tue, 30 Jun 2020 03:39:35: start model_add_line... INFO @ Tue, 30 Jun 2020 03:39:35: start X-correlation... INFO @ Tue, 30 Jun 2020 03:39:35: end of X-cor INFO @ Tue, 30 Jun 2020 03:39:35: #2 finished! INFO @ Tue, 30 Jun 2020 03:39:35: #2 predicted fragment length is 41 bps INFO @ Tue, 30 Jun 2020 03:39:35: #2 alternative fragment length(s) may be 2,41,158,445,573,591 bps INFO @ Tue, 30 Jun 2020 03:39:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981632/SRX3981632.10_model.r WARNING @ Tue, 30 Jun 2020 03:39:35: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:39:35: #2 You may need to consider one of the other alternative d(s): 2,41,158,445,573,591 WARNING @ Tue, 30 Jun 2020 03:39:35: #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 03:39:35: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:39:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:39:37: 30000000 INFO @ Tue, 30 Jun 2020 03:39:42: 31000000 INFO @ Tue, 30 Jun 2020 03:39:47: 32000000 INFO @ Tue, 30 Jun 2020 03:39:53: 33000000 INFO @ Tue, 30 Jun 2020 03:39:53: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:39:58: 34000000 INFO @ Tue, 30 Jun 2020 03:40:01: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:40:01: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:40:01: #1 total tags in treatment: 34587751 INFO @ Tue, 30 Jun 2020 03:40:01: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:40:01: #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 03:40:02: #1 tags after filtering in treatment: 34587710 INFO @ Tue, 30 Jun 2020 03:40:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:40:02: #1 finished! INFO @ Tue, 30 Jun 2020 03:40:02: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:40:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:40:04: #2 number of paired peaks: 146 WARNING @ Tue, 30 Jun 2020 03:40:04: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Tue, 30 Jun 2020 03:40:04: start model_add_line... INFO @ Tue, 30 Jun 2020 03:40:04: start X-correlation... INFO @ Tue, 30 Jun 2020 03:40:04: end of X-cor INFO @ Tue, 30 Jun 2020 03:40:04: #2 finished! INFO @ Tue, 30 Jun 2020 03:40:04: #2 predicted fragment length is 41 bps INFO @ Tue, 30 Jun 2020 03:40:04: #2 alternative fragment length(s) may be 2,41,158,445,573,591 bps INFO @ Tue, 30 Jun 2020 03:40:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981632/SRX3981632.20_model.r WARNING @ Tue, 30 Jun 2020 03:40:04: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:40:04: #2 You may need to consider one of the other alternative d(s): 2,41,158,445,573,591 WARNING @ Tue, 30 Jun 2020 03:40:04: #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 03:40:04: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:40:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:40:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981632/SRX3981632.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:40:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981632/SRX3981632.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:40:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981632/SRX3981632.05_summits.bed INFO @ Tue, 30 Jun 2020 03:40:18: Done! pass1 - making usageList (707 chroms): 1 millis pass2 - checking and writing primary data (3825 records, 4 fields): 23 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:40:28: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:40:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981632/SRX3981632.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:40:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981632/SRX3981632.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:40:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981632/SRX3981632.10_summits.bed INFO @ Tue, 30 Jun 2020 03:40:54: Done! pass1 - making usageList (517 chroms): 1 millis pass2 - checking and writing primary data (1999 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:40:58: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:41:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981632/SRX3981632.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:41:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981632/SRX3981632.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:41:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981632/SRX3981632.20_summits.bed INFO @ Tue, 30 Jun 2020 03:41:24: Done! pass1 - making usageList (191 chroms): 1 millis pass2 - checking and writing primary data (468 records, 4 fields): 6 millis CompletedMACS2peakCalling