Job ID = 14171846 SRX = SRX9008843 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16435127 spots for SRR12518315/SRR12518315.sra Written 16435127 spots for SRR12518315/SRR12518315.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172443 ("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: 00:30:59 16435127 reads; of these: 16435127 (100.00%) were paired; of these: 2815848 (17.13%) aligned concordantly 0 times 11403511 (69.38%) aligned concordantly exactly 1 time 2215768 (13.48%) aligned concordantly >1 times ---- 2815848 pairs aligned concordantly 0 times; of these: 1483623 (52.69%) aligned discordantly 1 time ---- 1332225 pairs aligned 0 times concordantly or discordantly; of these: 2664450 mates make up the pairs; of these: 1749328 (65.65%) aligned 0 times 388142 (14.57%) aligned exactly 1 time 526980 (19.78%) aligned >1 times 94.68% overall alignment rate Time searching: 00:30:59 Overall time: 00:31:00 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_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] 835326 / 14977935 = 0.0558 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 13:48:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9008843/SRX9008843.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9008843/SRX9008843.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9008843/SRX9008843.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9008843/SRX9008843.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 13:48:13: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:48:13: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:48:20: 1000000 INFO @ Sat, 11 Dec 2021 13:48:28: 2000000 INFO @ Sat, 11 Dec 2021 13:48:36: 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 13:48:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9008843/SRX9008843.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9008843/SRX9008843.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9008843/SRX9008843.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9008843/SRX9008843.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 13:48:43: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:48:43: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:48:44: 4000000 INFO @ Sat, 11 Dec 2021 13:48:52: 1000000 INFO @ Sat, 11 Dec 2021 13:48:52: 5000000 INFO @ Sat, 11 Dec 2021 13:49:00: 6000000 INFO @ Sat, 11 Dec 2021 13:49:01: 2000000 INFO @ Sat, 11 Dec 2021 13:49:09: 7000000 INFO @ Sat, 11 Dec 2021 13:49:09: 3000000 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 13:49:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9008843/SRX9008843.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9008843/SRX9008843.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9008843/SRX9008843.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9008843/SRX9008843.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 13:49:13: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:49:13: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:49:17: 8000000 INFO @ Sat, 11 Dec 2021 13:49:18: 4000000 INFO @ Sat, 11 Dec 2021 13:49:21: 1000000 INFO @ Sat, 11 Dec 2021 13:49:25: 9000000 INFO @ Sat, 11 Dec 2021 13:49:27: 5000000 INFO @ Sat, 11 Dec 2021 13:49:28: 2000000 INFO @ Sat, 11 Dec 2021 13:49:34: 10000000 INFO @ Sat, 11 Dec 2021 13:49:36: 6000000 INFO @ Sat, 11 Dec 2021 13:49:36: 3000000 INFO @ Sat, 11 Dec 2021 13:49:42: 11000000 INFO @ Sat, 11 Dec 2021 13:49:44: 4000000 INFO @ Sat, 11 Dec 2021 13:49:45: 7000000 INFO @ Sat, 11 Dec 2021 13:49:51: 12000000 INFO @ Sat, 11 Dec 2021 13:49:51: 5000000 INFO @ Sat, 11 Dec 2021 13:49:54: 8000000 INFO @ Sat, 11 Dec 2021 13:49:59: 6000000 INFO @ Sat, 11 Dec 2021 13:49:59: 13000000 INFO @ Sat, 11 Dec 2021 13:50:03: 9000000 INFO @ Sat, 11 Dec 2021 13:50:06: 7000000 INFO @ Sat, 11 Dec 2021 13:50:08: 14000000 INFO @ Sat, 11 Dec 2021 13:50:11: 10000000 INFO @ Sat, 11 Dec 2021 13:50:14: 8000000 INFO @ Sat, 11 Dec 2021 13:50:16: 15000000 INFO @ Sat, 11 Dec 2021 13:50:20: 11000000 INFO @ Sat, 11 Dec 2021 13:50:22: 9000000 INFO @ Sat, 11 Dec 2021 13:50:25: 16000000 INFO @ Sat, 11 Dec 2021 13:50:29: 12000000 INFO @ Sat, 11 Dec 2021 13:50:29: 10000000 INFO @ Sat, 11 Dec 2021 13:50:33: 17000000 INFO @ Sat, 11 Dec 2021 13:50:37: 11000000 INFO @ Sat, 11 Dec 2021 13:50:38: 13000000 INFO @ Sat, 11 Dec 2021 13:50:42: 18000000 INFO @ Sat, 11 Dec 2021 13:50:45: 12000000 INFO @ Sat, 11 Dec 2021 13:50:47: 14000000 INFO @ Sat, 11 Dec 2021 13:50:50: 19000000 INFO @ Sat, 11 Dec 2021 13:50:52: 13000000 INFO @ Sat, 11 Dec 2021 13:50:56: 15000000 INFO @ Sat, 11 Dec 2021 13:50:59: 20000000 INFO @ Sat, 11 Dec 2021 13:51:00: 14000000 INFO @ Sat, 11 Dec 2021 13:51:05: 16000000 INFO @ Sat, 11 Dec 2021 13:51:07: 21000000 INFO @ Sat, 11 Dec 2021 13:51:07: 15000000 INFO @ Sat, 11 Dec 2021 13:51:13: 17000000 INFO @ Sat, 11 Dec 2021 13:51:15: 16000000 INFO @ Sat, 11 Dec 2021 13:51:15: 22000000 INFO @ Sat, 11 Dec 2021 13:51:22: 18000000 INFO @ Sat, 11 Dec 2021 13:51:23: 17000000 INFO @ Sat, 11 Dec 2021 13:51:24: 23000000 INFO @ Sat, 11 Dec 2021 13:51:30: 18000000 INFO @ Sat, 11 Dec 2021 13:51:31: 19000000 INFO @ Sat, 11 Dec 2021 13:51:32: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:51:38: 19000000 INFO @ Sat, 11 Dec 2021 13:51:40: 20000000 INFO @ Sat, 11 Dec 2021 13:51:41: 25000000 INFO @ Sat, 11 Dec 2021 13:51:45: 20000000 INFO @ Sat, 11 Dec 2021 13:51:49: 21000000 INFO @ Sat, 11 Dec 2021 13:51:49: 26000000 INFO @ Sat, 11 Dec 2021 13:51:53: 21000000 INFO @ Sat, 11 Dec 2021 13:51:57: 27000000 INFO @ Sat, 11 Dec 2021 13:51:58: 22000000 INFO @ Sat, 11 Dec 2021 13:52:01: 22000000 INFO @ Sat, 11 Dec 2021 13:52:06: 28000000 INFO @ Sat, 11 Dec 2021 13:52:07: 23000000 INFO @ Sat, 11 Dec 2021 13:52:09: 23000000 INFO @ Sat, 11 Dec 2021 13:52:14: 29000000 INFO @ Sat, 11 Dec 2021 13:52:16: 24000000 INFO @ Sat, 11 Dec 2021 13:52:17: 24000000 INFO @ Sat, 11 Dec 2021 13:52:18: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 13:52:18: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 13:52:18: #1 total tags in treatment: 12854213 INFO @ Sat, 11 Dec 2021 13:52:18: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:52:18: #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 13:52:18: #1 tags after filtering in treatment: 12449605 INFO @ Sat, 11 Dec 2021 13:52:18: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 13:52:18: #1 finished! INFO @ Sat, 11 Dec 2021 13:52:18: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:52:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:52:19: #2 number of paired peaks: 127 WARNING @ Sat, 11 Dec 2021 13:52:19: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Sat, 11 Dec 2021 13:52:19: start model_add_line... INFO @ Sat, 11 Dec 2021 13:52:19: start X-correlation... INFO @ Sat, 11 Dec 2021 13:52:19: end of X-cor INFO @ Sat, 11 Dec 2021 13:52:19: #2 finished! INFO @ Sat, 11 Dec 2021 13:52:19: #2 predicted fragment length is 187 bps INFO @ Sat, 11 Dec 2021 13:52:19: #2 alternative fragment length(s) may be 4,158,187,585 bps INFO @ Sat, 11 Dec 2021 13:52:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9008843/SRX9008843.05_model.r WARNING @ Sat, 11 Dec 2021 13:52:19: #2 Since the d (187) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:52:19: #2 You may need to consider one of the other alternative d(s): 4,158,187,585 WARNING @ Sat, 11 Dec 2021 13:52:19: #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 13:52:19: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:52:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:52:24: 25000000 INFO @ Sat, 11 Dec 2021 13:52:25: 25000000 INFO @ Sat, 11 Dec 2021 13:52:34: 26000000 INFO @ Sat, 11 Dec 2021 13:52:34: 26000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:52:43: 27000000 INFO @ Sat, 11 Dec 2021 13:52:43: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:52:43: 27000000 INFO @ Sat, 11 Dec 2021 13:52:52: 28000000 INFO @ Sat, 11 Dec 2021 13:52:53: 28000000 INFO @ Sat, 11 Dec 2021 13:52:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9008843/SRX9008843.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:52:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9008843/SRX9008843.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:52:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9008843/SRX9008843.05_summits.bed INFO @ Sat, 11 Dec 2021 13:52:54: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (309 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:53:02: 29000000 INFO @ Sat, 11 Dec 2021 13:53:02: 29000000 INFO @ Sat, 11 Dec 2021 13:53:06: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 13:53:06: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 13:53:06: #1 total tags in treatment: 12854213 INFO @ Sat, 11 Dec 2021 13:53:06: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:53:06: #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 13:53:06: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 13:53:06: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 13:53:06: #1 total tags in treatment: 12854213 INFO @ Sat, 11 Dec 2021 13:53:06: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:53:06: #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 13:53:06: #1 tags after filtering in treatment: 12449605 INFO @ Sat, 11 Dec 2021 13:53:06: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 13:53:06: #1 finished! INFO @ Sat, 11 Dec 2021 13:53:06: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:53:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:53:06: #1 tags after filtering in treatment: 12449605 INFO @ Sat, 11 Dec 2021 13:53:06: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 13:53:06: #1 finished! INFO @ Sat, 11 Dec 2021 13:53:06: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:53:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:53:07: #2 number of paired peaks: 127 WARNING @ Sat, 11 Dec 2021 13:53:07: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Sat, 11 Dec 2021 13:53:07: start model_add_line... INFO @ Sat, 11 Dec 2021 13:53:07: start X-correlation... INFO @ Sat, 11 Dec 2021 13:53:07: end of X-cor INFO @ Sat, 11 Dec 2021 13:53:07: #2 finished! INFO @ Sat, 11 Dec 2021 13:53:07: #2 predicted fragment length is 187 bps INFO @ Sat, 11 Dec 2021 13:53:07: #2 alternative fragment length(s) may be 4,158,187,585 bps INFO @ Sat, 11 Dec 2021 13:53:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9008843/SRX9008843.10_model.r WARNING @ Sat, 11 Dec 2021 13:53:07: #2 Since the d (187) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:53:07: #2 You may need to consider one of the other alternative d(s): 4,158,187,585 WARNING @ Sat, 11 Dec 2021 13:53:07: #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 13:53:07: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:53:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:53:07: #2 number of paired peaks: 127 WARNING @ Sat, 11 Dec 2021 13:53:07: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Sat, 11 Dec 2021 13:53:07: start model_add_line... INFO @ Sat, 11 Dec 2021 13:53:07: start X-correlation... INFO @ Sat, 11 Dec 2021 13:53:07: end of X-cor INFO @ Sat, 11 Dec 2021 13:53:07: #2 finished! INFO @ Sat, 11 Dec 2021 13:53:07: #2 predicted fragment length is 187 bps INFO @ Sat, 11 Dec 2021 13:53:07: #2 alternative fragment length(s) may be 4,158,187,585 bps INFO @ Sat, 11 Dec 2021 13:53:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9008843/SRX9008843.20_model.r WARNING @ Sat, 11 Dec 2021 13:53:07: #2 Since the d (187) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:53:07: #2 You may need to consider one of the other alternative d(s): 4,158,187,585 WARNING @ Sat, 11 Dec 2021 13:53:07: #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 13:53:07: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:53:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:53:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:53:32: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:53:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9008843/SRX9008843.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:53:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9008843/SRX9008843.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:53:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9008843/SRX9008843.20_summits.bed INFO @ Sat, 11 Dec 2021 13:53:42: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (61 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:53:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9008843/SRX9008843.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:53:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9008843/SRX9008843.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:53:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9008843/SRX9008843.10_summits.bed INFO @ Sat, 11 Dec 2021 13:53:43: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (141 records, 4 fields): 1 millis CompletedMACS2peakCalling