Job ID = 16438595 SRX = SRX10031695 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 31828133 spots for SRR13634465/SRR13634465.sra Written 31828133 spots for SRR13634465/SRR13634465.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438965 ("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: 00:12:14 31828133 reads; of these: 31828133 (100.00%) were unpaired; of these: 846475 (2.66%) aligned 0 times 24289124 (76.31%) aligned exactly 1 time 6692534 (21.03%) aligned >1 times 97.34% overall alignment rate Time searching: 00:12:15 Overall time: 00:12:15 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 16 files... [bam_rmdupse_core] 5834969 / 30981658 = 0.1883 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:21:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031695/SRX10031695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031695/SRX10031695.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031695/SRX10031695.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10031695/SRX10031695.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, 02 Aug 2022 14:21:36: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:21:36: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:21:42: 1000000 INFO @ Tue, 02 Aug 2022 14:21:47: 2000000 INFO @ Tue, 02 Aug 2022 14:21:53: 3000000 INFO @ Tue, 02 Aug 2022 14:21:58: 4000000 INFO @ Tue, 02 Aug 2022 14:22:04: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:22:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031695/SRX10031695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031695/SRX10031695.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031695/SRX10031695.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10031695/SRX10031695.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, 02 Aug 2022 14:22:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:22:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:22:10: 6000000 INFO @ Tue, 02 Aug 2022 14:22:14: 1000000 INFO @ Tue, 02 Aug 2022 14:22:15: 7000000 INFO @ Tue, 02 Aug 2022 14:22:21: 2000000 INFO @ Tue, 02 Aug 2022 14:22:21: 8000000 INFO @ Tue, 02 Aug 2022 14:22:27: 9000000 INFO @ Tue, 02 Aug 2022 14:22:27: 3000000 INFO @ Tue, 02 Aug 2022 14:22:33: 10000000 INFO @ Tue, 02 Aug 2022 14:22:34: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:22:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031695/SRX10031695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031695/SRX10031695.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031695/SRX10031695.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10031695/SRX10031695.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, 02 Aug 2022 14:22:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:22:37: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:22:39: 11000000 INFO @ Tue, 02 Aug 2022 14:22:40: 5000000 INFO @ Tue, 02 Aug 2022 14:22:42: 1000000 INFO @ Tue, 02 Aug 2022 14:22:45: 12000000 INFO @ Tue, 02 Aug 2022 14:22:47: 6000000 INFO @ Tue, 02 Aug 2022 14:22:48: 2000000 INFO @ Tue, 02 Aug 2022 14:22:51: 13000000 INFO @ Tue, 02 Aug 2022 14:22:54: 7000000 INFO @ Tue, 02 Aug 2022 14:22:54: 3000000 INFO @ Tue, 02 Aug 2022 14:22:56: 14000000 INFO @ Tue, 02 Aug 2022 14:23:00: 4000000 INFO @ Tue, 02 Aug 2022 14:23:01: 8000000 INFO @ Tue, 02 Aug 2022 14:23:02: 15000000 INFO @ Tue, 02 Aug 2022 14:23:06: 5000000 INFO @ Tue, 02 Aug 2022 14:23:08: 9000000 INFO @ Tue, 02 Aug 2022 14:23:08: 16000000 INFO @ Tue, 02 Aug 2022 14:23:12: 6000000 INFO @ Tue, 02 Aug 2022 14:23:14: 17000000 INFO @ Tue, 02 Aug 2022 14:23:15: 10000000 INFO @ Tue, 02 Aug 2022 14:23:18: 7000000 INFO @ Tue, 02 Aug 2022 14:23:20: 18000000 INFO @ Tue, 02 Aug 2022 14:23:22: 11000000 INFO @ Tue, 02 Aug 2022 14:23:24: 8000000 INFO @ Tue, 02 Aug 2022 14:23:26: 19000000 INFO @ Tue, 02 Aug 2022 14:23:28: 12000000 INFO @ Tue, 02 Aug 2022 14:23:30: 9000000 INFO @ Tue, 02 Aug 2022 14:23:32: 20000000 INFO @ Tue, 02 Aug 2022 14:23:35: 13000000 INFO @ Tue, 02 Aug 2022 14:23:35: 10000000 INFO @ Tue, 02 Aug 2022 14:23:37: 21000000 INFO @ Tue, 02 Aug 2022 14:23:41: 11000000 INFO @ Tue, 02 Aug 2022 14:23:42: 14000000 INFO @ Tue, 02 Aug 2022 14:23:43: 22000000 INFO @ Tue, 02 Aug 2022 14:23:47: 12000000 INFO @ Tue, 02 Aug 2022 14:23:49: 15000000 INFO @ Tue, 02 Aug 2022 14:23:49: 23000000 INFO @ Tue, 02 Aug 2022 14:23:53: 13000000 INFO @ Tue, 02 Aug 2022 14:23:55: 24000000 INFO @ Tue, 02 Aug 2022 14:23:56: 16000000 INFO @ Tue, 02 Aug 2022 14:23:59: 14000000 INFO @ Tue, 02 Aug 2022 14:24:01: 25000000 INFO @ Tue, 02 Aug 2022 14:24:02: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:24:02: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:24:02: #1 total tags in treatment: 25146689 INFO @ Tue, 02 Aug 2022 14:24:02: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:24:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:24:02: #1 tags after filtering in treatment: 25146689 INFO @ Tue, 02 Aug 2022 14:24:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:24:02: #1 finished! INFO @ Tue, 02 Aug 2022 14:24:02: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:24:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:24:03: 17000000 INFO @ Tue, 02 Aug 2022 14:24:04: #2 number of paired peaks: 131 WARNING @ Tue, 02 Aug 2022 14:24:04: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Tue, 02 Aug 2022 14:24:04: start model_add_line... INFO @ Tue, 02 Aug 2022 14:24:04: start X-correlation... INFO @ Tue, 02 Aug 2022 14:24:04: end of X-cor INFO @ Tue, 02 Aug 2022 14:24:04: #2 finished! INFO @ Tue, 02 Aug 2022 14:24:04: #2 predicted fragment length is 75 bps INFO @ Tue, 02 Aug 2022 14:24:04: #2 alternative fragment length(s) may be 1,23,75,131,490,496,531,567 bps INFO @ Tue, 02 Aug 2022 14:24:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031695/SRX10031695.05_model.r WARNING @ Tue, 02 Aug 2022 14:24:04: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:24:04: #2 You may need to consider one of the other alternative d(s): 1,23,75,131,490,496,531,567 WARNING @ Tue, 02 Aug 2022 14:24:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:24:04: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:24:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:24:05: 15000000 INFO @ Tue, 02 Aug 2022 14:24:09: 18000000 INFO @ Tue, 02 Aug 2022 14:24:11: 16000000 INFO @ Tue, 02 Aug 2022 14:24:16: 19000000 INFO @ Tue, 02 Aug 2022 14:24:16: 17000000 INFO @ Tue, 02 Aug 2022 14:24:22: 18000000 INFO @ Tue, 02 Aug 2022 14:24:23: 20000000 INFO @ Tue, 02 Aug 2022 14:24:28: 19000000 INFO @ Tue, 02 Aug 2022 14:24:30: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:24:34: 20000000 INFO @ Tue, 02 Aug 2022 14:24:37: 22000000 INFO @ Tue, 02 Aug 2022 14:24:40: 21000000 INFO @ Tue, 02 Aug 2022 14:24:44: 23000000 INFO @ Tue, 02 Aug 2022 14:24:45: 22000000 INFO @ Tue, 02 Aug 2022 14:24:47: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:24:50: 24000000 INFO @ Tue, 02 Aug 2022 14:24:51: 23000000 INFO @ Tue, 02 Aug 2022 14:24:57: 24000000 INFO @ Tue, 02 Aug 2022 14:24:57: 25000000 INFO @ Tue, 02 Aug 2022 14:24:58: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:24:58: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:24:58: #1 total tags in treatment: 25146689 INFO @ Tue, 02 Aug 2022 14:24:58: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:24:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:24:59: #1 tags after filtering in treatment: 25146689 INFO @ Tue, 02 Aug 2022 14:24:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:24:59: #1 finished! INFO @ Tue, 02 Aug 2022 14:24:59: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:24:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:25:00: #2 number of paired peaks: 131 WARNING @ Tue, 02 Aug 2022 14:25:00: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Tue, 02 Aug 2022 14:25:00: start model_add_line... INFO @ Tue, 02 Aug 2022 14:25:00: start X-correlation... INFO @ Tue, 02 Aug 2022 14:25:00: end of X-cor INFO @ Tue, 02 Aug 2022 14:25:00: #2 finished! INFO @ Tue, 02 Aug 2022 14:25:00: #2 predicted fragment length is 75 bps INFO @ Tue, 02 Aug 2022 14:25:00: #2 alternative fragment length(s) may be 1,23,75,131,490,496,531,567 bps INFO @ Tue, 02 Aug 2022 14:25:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031695/SRX10031695.10_model.r WARNING @ Tue, 02 Aug 2022 14:25:00: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:25:00: #2 You may need to consider one of the other alternative d(s): 1,23,75,131,490,496,531,567 WARNING @ Tue, 02 Aug 2022 14:25:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:25:00: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:25:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:25:03: 25000000 INFO @ Tue, 02 Aug 2022 14:25:04: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:25:04: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:25:04: #1 total tags in treatment: 25146689 INFO @ Tue, 02 Aug 2022 14:25:04: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:25:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:25:04: #1 tags after filtering in treatment: 25146689 INFO @ Tue, 02 Aug 2022 14:25:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:25:04: #1 finished! INFO @ Tue, 02 Aug 2022 14:25:04: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:25:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:25:06: #2 number of paired peaks: 131 WARNING @ Tue, 02 Aug 2022 14:25:06: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Tue, 02 Aug 2022 14:25:06: start model_add_line... INFO @ Tue, 02 Aug 2022 14:25:06: start X-correlation... INFO @ Tue, 02 Aug 2022 14:25:06: end of X-cor INFO @ Tue, 02 Aug 2022 14:25:06: #2 finished! INFO @ Tue, 02 Aug 2022 14:25:06: #2 predicted fragment length is 75 bps INFO @ Tue, 02 Aug 2022 14:25:06: #2 alternative fragment length(s) may be 1,23,75,131,490,496,531,567 bps INFO @ Tue, 02 Aug 2022 14:25:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031695/SRX10031695.20_model.r WARNING @ Tue, 02 Aug 2022 14:25:06: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:25:06: #2 You may need to consider one of the other alternative d(s): 1,23,75,131,490,496,531,567 WARNING @ Tue, 02 Aug 2022 14:25:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:25:06: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:25:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:25:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031695/SRX10031695.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:25:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031695/SRX10031695.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:25:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031695/SRX10031695.05_summits.bed INFO @ Tue, 02 Aug 2022 14:25:09: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1133 records, 4 fields): 20 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:25:42: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:25:47: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:26:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031695/SRX10031695.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:26:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031695/SRX10031695.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:26:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031695/SRX10031695.10_summits.bed INFO @ Tue, 02 Aug 2022 14:26:04: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (622 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:26:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031695/SRX10031695.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:26:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031695/SRX10031695.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:26:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031695/SRX10031695.20_summits.bed INFO @ Tue, 02 Aug 2022 14:26:09: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (345 records, 4 fields): 75 millis CompletedMACS2peakCalling