Job ID = 14170148 SRX = SRX8556382 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 25599672 spots for SRR12024938/SRR12024938.sra Written 25599672 spots for SRR12024938/SRR12024938.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170917 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:18:01 25599672 reads; of these: 25599672 (100.00%) were paired; of these: 12032650 (47.00%) aligned concordantly 0 times 9275264 (36.23%) aligned concordantly exactly 1 time 4291758 (16.76%) aligned concordantly >1 times ---- 12032650 pairs aligned concordantly 0 times; of these: 4681645 (38.91%) aligned discordantly 1 time ---- 7351005 pairs aligned 0 times concordantly or discordantly; of these: 14702010 mates make up the pairs; of these: 10536207 (71.67%) aligned 0 times 722838 (4.92%) aligned exactly 1 time 3442965 (23.42%) aligned >1 times 79.42% overall alignment rate Time searching: 01:18:01 Overall time: 01:18:01 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 32 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 2122040 / 17973857 = 0.1181 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 07:22:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556382/SRX8556382.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556382/SRX8556382.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556382/SRX8556382.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556382/SRX8556382.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 07:22:28: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:22:28: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:22:37: 1000000 INFO @ Sat, 11 Dec 2021 07:22:45: 2000000 INFO @ Sat, 11 Dec 2021 07:22:54: 3000000 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 07:22:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556382/SRX8556382.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556382/SRX8556382.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556382/SRX8556382.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556382/SRX8556382.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 07:22:58: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:22:58: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:23:04: 4000000 INFO @ Sat, 11 Dec 2021 07:23:09: 1000000 INFO @ Sat, 11 Dec 2021 07:23:14: 5000000 INFO @ Sat, 11 Dec 2021 07:23:19: 2000000 INFO @ Sat, 11 Dec 2021 07:23:25: 6000000 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 07:23:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556382/SRX8556382.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556382/SRX8556382.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556382/SRX8556382.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556382/SRX8556382.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 07:23:28: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:23:28: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:23:30: 3000000 INFO @ Sat, 11 Dec 2021 07:23:35: 7000000 INFO @ Sat, 11 Dec 2021 07:23:38: 1000000 INFO @ Sat, 11 Dec 2021 07:23:41: 4000000 INFO @ Sat, 11 Dec 2021 07:23:46: 8000000 INFO @ Sat, 11 Dec 2021 07:23:49: 2000000 INFO @ Sat, 11 Dec 2021 07:23:52: 5000000 INFO @ Sat, 11 Dec 2021 07:23:57: 9000000 INFO @ Sat, 11 Dec 2021 07:24:00: 3000000 INFO @ Sat, 11 Dec 2021 07:24:03: 6000000 INFO @ Sat, 11 Dec 2021 07:24:07: 10000000 INFO @ Sat, 11 Dec 2021 07:24:11: 4000000 INFO @ Sat, 11 Dec 2021 07:24:14: 7000000 INFO @ Sat, 11 Dec 2021 07:24:18: 11000000 INFO @ Sat, 11 Dec 2021 07:24:22: 5000000 INFO @ Sat, 11 Dec 2021 07:24:25: 8000000 INFO @ Sat, 11 Dec 2021 07:24:29: 12000000 INFO @ Sat, 11 Dec 2021 07:24:33: 6000000 INFO @ Sat, 11 Dec 2021 07:24:36: 9000000 INFO @ Sat, 11 Dec 2021 07:24:40: 13000000 INFO @ Sat, 11 Dec 2021 07:24:44: 7000000 INFO @ Sat, 11 Dec 2021 07:24:47: 10000000 INFO @ Sat, 11 Dec 2021 07:24:51: 14000000 INFO @ Sat, 11 Dec 2021 07:24:56: 8000000 INFO @ Sat, 11 Dec 2021 07:24:59: 11000000 INFO @ Sat, 11 Dec 2021 07:25:05: 15000000 INFO @ Sat, 11 Dec 2021 07:25:08: 9000000 INFO @ Sat, 11 Dec 2021 07:25:11: 12000000 INFO @ Sat, 11 Dec 2021 07:25:16: 16000000 INFO @ Sat, 11 Dec 2021 07:25:20: 10000000 INFO @ Sat, 11 Dec 2021 07:25:23: 13000000 INFO @ Sat, 11 Dec 2021 07:25:29: 17000000 INFO @ Sat, 11 Dec 2021 07:25:33: 11000000 INFO @ Sat, 11 Dec 2021 07:25:36: 14000000 INFO @ Sat, 11 Dec 2021 07:25:41: 18000000 INFO @ Sat, 11 Dec 2021 07:25:45: 12000000 INFO @ Sat, 11 Dec 2021 07:25:48: 15000000 INFO @ Sat, 11 Dec 2021 07:25:55: 19000000 INFO @ Sat, 11 Dec 2021 07:25:58: 13000000 INFO @ Sat, 11 Dec 2021 07:26:00: 16000000 INFO @ Sat, 11 Dec 2021 07:26:09: 20000000 INFO @ Sat, 11 Dec 2021 07:26:10: 14000000 INFO @ Sat, 11 Dec 2021 07:26:13: 17000000 INFO @ Sat, 11 Dec 2021 07:26:23: 21000000 INFO @ Sat, 11 Dec 2021 07:26:23: 15000000 INFO @ Sat, 11 Dec 2021 07:26:26: 18000000 INFO @ Sat, 11 Dec 2021 07:26:36: 16000000 INFO @ Sat, 11 Dec 2021 07:26:37: 22000000 INFO @ Sat, 11 Dec 2021 07:26:38: 19000000 INFO @ Sat, 11 Dec 2021 07:26:48: 17000000 INFO @ Sat, 11 Dec 2021 07:26:51: 23000000 INFO @ Sat, 11 Dec 2021 07:26:51: 20000000 INFO @ Sat, 11 Dec 2021 07:27:00: 18000000 INFO @ Sat, 11 Dec 2021 07:27:03: 21000000 INFO @ Sat, 11 Dec 2021 07:27:03: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:27:12: 19000000 INFO @ Sat, 11 Dec 2021 07:27:15: 22000000 INFO @ Sat, 11 Dec 2021 07:27:15: 25000000 INFO @ Sat, 11 Dec 2021 07:27:24: 20000000 INFO @ Sat, 11 Dec 2021 07:27:26: 23000000 INFO @ Sat, 11 Dec 2021 07:27:26: 26000000 INFO @ Sat, 11 Dec 2021 07:27:36: 21000000 INFO @ Sat, 11 Dec 2021 07:27:37: 24000000 INFO @ Sat, 11 Dec 2021 07:27:38: 27000000 INFO @ Sat, 11 Dec 2021 07:27:47: 22000000 INFO @ Sat, 11 Dec 2021 07:27:48: 25000000 INFO @ Sat, 11 Dec 2021 07:27:49: 28000000 INFO @ Sat, 11 Dec 2021 07:27:58: 23000000 INFO @ Sat, 11 Dec 2021 07:27:59: 26000000 INFO @ Sat, 11 Dec 2021 07:28:01: 29000000 INFO @ Sat, 11 Dec 2021 07:28:09: 24000000 INFO @ Sat, 11 Dec 2021 07:28:10: 27000000 INFO @ Sat, 11 Dec 2021 07:28:12: 30000000 INFO @ Sat, 11 Dec 2021 07:28:20: 25000000 INFO @ Sat, 11 Dec 2021 07:28:21: 28000000 INFO @ Sat, 11 Dec 2021 07:28:23: 31000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:28:31: 26000000 INFO @ Sat, 11 Dec 2021 07:28:32: 29000000 INFO @ Sat, 11 Dec 2021 07:28:34: 32000000 INFO @ Sat, 11 Dec 2021 07:28:42: 27000000 INFO @ Sat, 11 Dec 2021 07:28:43: 30000000 INFO @ Sat, 11 Dec 2021 07:28:45: 33000000 INFO @ Sat, 11 Dec 2021 07:28:53: 28000000 INFO @ Sat, 11 Dec 2021 07:28:54: 31000000 INFO @ Sat, 11 Dec 2021 07:28:56: 34000000 INFO @ Sat, 11 Dec 2021 07:29:04: 29000000 INFO @ Sat, 11 Dec 2021 07:29:04: 32000000 INFO @ Sat, 11 Dec 2021 07:29:07: 35000000 INFO @ Sat, 11 Dec 2021 07:29:15: 33000000 INFO @ Sat, 11 Dec 2021 07:29:15: 30000000 INFO @ Sat, 11 Dec 2021 07:29:17: 36000000 INFO @ Sat, 11 Dec 2021 07:29:22: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 07:29:22: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 07:29:22: #1 total tags in treatment: 11846603 INFO @ Sat, 11 Dec 2021 07:29:22: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:29:22: #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 07:29:22: #1 tags after filtering in treatment: 11111004 INFO @ Sat, 11 Dec 2021 07:29:22: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 07:29:22: #1 finished! INFO @ Sat, 11 Dec 2021 07:29:22: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:29:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:29:23: #2 number of paired peaks: 159 WARNING @ Sat, 11 Dec 2021 07:29:23: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Sat, 11 Dec 2021 07:29:23: start model_add_line... INFO @ Sat, 11 Dec 2021 07:29:23: start X-correlation... INFO @ Sat, 11 Dec 2021 07:29:23: end of X-cor INFO @ Sat, 11 Dec 2021 07:29:23: #2 finished! INFO @ Sat, 11 Dec 2021 07:29:23: #2 predicted fragment length is 185 bps INFO @ Sat, 11 Dec 2021 07:29:23: #2 alternative fragment length(s) may be 185 bps INFO @ Sat, 11 Dec 2021 07:29:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556382/SRX8556382.05_model.r WARNING @ Sat, 11 Dec 2021 07:29:23: #2 Since the d (185) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:29:23: #2 You may need to consider one of the other alternative d(s): 185 WARNING @ Sat, 11 Dec 2021 07:29:23: #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 07:29:23: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:29:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:29:26: 34000000 INFO @ Sat, 11 Dec 2021 07:29:26: 31000000 INFO @ Sat, 11 Dec 2021 07:29:37: 35000000 INFO @ Sat, 11 Dec 2021 07:29:37: 32000000 INFO @ Sat, 11 Dec 2021 07:29:46: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:29:47: 36000000 INFO @ Sat, 11 Dec 2021 07:29:48: 33000000 INFO @ Sat, 11 Dec 2021 07:29:51: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 07:29:51: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 07:29:51: #1 total tags in treatment: 11846603 INFO @ Sat, 11 Dec 2021 07:29:51: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:29:51: #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 07:29:52: #1 tags after filtering in treatment: 11111004 INFO @ Sat, 11 Dec 2021 07:29:52: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 07:29:52: #1 finished! INFO @ Sat, 11 Dec 2021 07:29:52: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:29:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:29:52: #2 number of paired peaks: 159 WARNING @ Sat, 11 Dec 2021 07:29:52: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Sat, 11 Dec 2021 07:29:52: start model_add_line... INFO @ Sat, 11 Dec 2021 07:29:53: start X-correlation... INFO @ Sat, 11 Dec 2021 07:29:53: end of X-cor INFO @ Sat, 11 Dec 2021 07:29:53: #2 finished! INFO @ Sat, 11 Dec 2021 07:29:53: #2 predicted fragment length is 185 bps INFO @ Sat, 11 Dec 2021 07:29:53: #2 alternative fragment length(s) may be 185 bps INFO @ Sat, 11 Dec 2021 07:29:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556382/SRX8556382.10_model.r WARNING @ Sat, 11 Dec 2021 07:29:53: #2 Since the d (185) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:29:53: #2 You may need to consider one of the other alternative d(s): 185 WARNING @ Sat, 11 Dec 2021 07:29:53: #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 07:29:53: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:29:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:29:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556382/SRX8556382.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:29:58: 34000000 INFO @ Sat, 11 Dec 2021 07:29:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556382/SRX8556382.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:29:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556382/SRX8556382.05_summits.bed INFO @ Sat, 11 Dec 2021 07:29:58: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2805 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:30:07: 35000000 INFO @ Sat, 11 Dec 2021 07:30:15: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:30:16: 36000000 INFO @ Sat, 11 Dec 2021 07:30:19: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 07:30:19: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 07:30:19: #1 total tags in treatment: 11846603 INFO @ Sat, 11 Dec 2021 07:30:19: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:30:19: #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 07:30:20: #1 tags after filtering in treatment: 11111004 INFO @ Sat, 11 Dec 2021 07:30:20: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 07:30:20: #1 finished! INFO @ Sat, 11 Dec 2021 07:30:20: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:30:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:30:20: #2 number of paired peaks: 159 WARNING @ Sat, 11 Dec 2021 07:30:20: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Sat, 11 Dec 2021 07:30:20: start model_add_line... INFO @ Sat, 11 Dec 2021 07:30:20: start X-correlation... INFO @ Sat, 11 Dec 2021 07:30:20: end of X-cor INFO @ Sat, 11 Dec 2021 07:30:20: #2 finished! INFO @ Sat, 11 Dec 2021 07:30:20: #2 predicted fragment length is 185 bps INFO @ Sat, 11 Dec 2021 07:30:20: #2 alternative fragment length(s) may be 185 bps INFO @ Sat, 11 Dec 2021 07:30:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556382/SRX8556382.20_model.r WARNING @ Sat, 11 Dec 2021 07:30:20: #2 Since the d (185) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:30:20: #2 You may need to consider one of the other alternative d(s): 185 WARNING @ Sat, 11 Dec 2021 07:30:20: #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 07:30:20: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:30:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:30:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556382/SRX8556382.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:30:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556382/SRX8556382.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:30:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556382/SRX8556382.10_summits.bed INFO @ Sat, 11 Dec 2021 07:30:26: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1383 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:30:42: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:30:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556382/SRX8556382.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:30:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556382/SRX8556382.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:30:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556382/SRX8556382.20_summits.bed INFO @ Sat, 11 Dec 2021 07:30:53: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (591 records, 4 fields): 1 millis CompletedMACS2peakCalling