Job ID = 12265576 SRX = SRX7277030 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 27001724 spots for SRR10597295/SRR10597295.sra Written 27001724 spots for SRR10597295/SRR10597295.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265828 ("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: 00:36:51 27001724 reads; of these: 27001724 (100.00%) were paired; of these: 10647657 (39.43%) aligned concordantly 0 times 11405515 (42.24%) aligned concordantly exactly 1 time 4948552 (18.33%) aligned concordantly >1 times ---- 10647657 pairs aligned concordantly 0 times; of these: 2718430 (25.53%) aligned discordantly 1 time ---- 7929227 pairs aligned 0 times concordantly or discordantly; of these: 15858454 mates make up the pairs; of these: 12912779 (81.43%) aligned 0 times 781523 (4.93%) aligned exactly 1 time 2164152 (13.65%) aligned >1 times 76.09% overall alignment rate Time searching: 00:36:51 Overall time: 00:36:51 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 20 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] 3074635 / 18922548 = 0.1625 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:32:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277030/SRX7277030.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277030/SRX7277030.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277030/SRX7277030.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277030/SRX7277030.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, 03 Apr 2021 08:32:21: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:32:21: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:32:27: 1000000 INFO @ Sat, 03 Apr 2021 08:32:34: 2000000 INFO @ Sat, 03 Apr 2021 08:32:40: 3000000 INFO @ Sat, 03 Apr 2021 08:32:47: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:32:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277030/SRX7277030.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277030/SRX7277030.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277030/SRX7277030.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277030/SRX7277030.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, 03 Apr 2021 08:32:51: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:32:51: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:32:54: 5000000 INFO @ Sat, 03 Apr 2021 08:32:58: 1000000 INFO @ Sat, 03 Apr 2021 08:33:01: 6000000 INFO @ Sat, 03 Apr 2021 08:33:06: 2000000 INFO @ Sat, 03 Apr 2021 08:33:09: 7000000 INFO @ Sat, 03 Apr 2021 08:33:13: 3000000 INFO @ Sat, 03 Apr 2021 08:33:16: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:33:20: 4000000 INFO @ Sat, 03 Apr 2021 08:33:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277030/SRX7277030.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277030/SRX7277030.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277030/SRX7277030.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277030/SRX7277030.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, 03 Apr 2021 08:33:21: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:33:21: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:33:23: 9000000 INFO @ Sat, 03 Apr 2021 08:33:28: 5000000 INFO @ Sat, 03 Apr 2021 08:33:28: 1000000 INFO @ Sat, 03 Apr 2021 08:33:31: 10000000 INFO @ Sat, 03 Apr 2021 08:33:35: 6000000 INFO @ Sat, 03 Apr 2021 08:33:36: 2000000 INFO @ Sat, 03 Apr 2021 08:33:38: 11000000 INFO @ Sat, 03 Apr 2021 08:33:43: 7000000 INFO @ Sat, 03 Apr 2021 08:33:43: 3000000 INFO @ Sat, 03 Apr 2021 08:33:46: 12000000 INFO @ Sat, 03 Apr 2021 08:33:50: 8000000 INFO @ Sat, 03 Apr 2021 08:33:51: 4000000 INFO @ Sat, 03 Apr 2021 08:33:53: 13000000 INFO @ Sat, 03 Apr 2021 08:33:58: 9000000 INFO @ Sat, 03 Apr 2021 08:33:58: 5000000 INFO @ Sat, 03 Apr 2021 08:34:00: 14000000 INFO @ Sat, 03 Apr 2021 08:34:05: 10000000 INFO @ Sat, 03 Apr 2021 08:34:05: 6000000 INFO @ Sat, 03 Apr 2021 08:34:08: 15000000 INFO @ Sat, 03 Apr 2021 08:34:13: 11000000 INFO @ Sat, 03 Apr 2021 08:34:13: 7000000 INFO @ Sat, 03 Apr 2021 08:34:15: 16000000 INFO @ Sat, 03 Apr 2021 08:34:20: 12000000 INFO @ Sat, 03 Apr 2021 08:34:20: 8000000 INFO @ Sat, 03 Apr 2021 08:34:22: 17000000 INFO @ Sat, 03 Apr 2021 08:34:28: 13000000 INFO @ Sat, 03 Apr 2021 08:34:28: 9000000 INFO @ Sat, 03 Apr 2021 08:34:30: 18000000 INFO @ Sat, 03 Apr 2021 08:34:35: 14000000 INFO @ Sat, 03 Apr 2021 08:34:35: 10000000 INFO @ Sat, 03 Apr 2021 08:34:37: 19000000 INFO @ Sat, 03 Apr 2021 08:34:43: 15000000 INFO @ Sat, 03 Apr 2021 08:34:43: 11000000 INFO @ Sat, 03 Apr 2021 08:34:44: 20000000 INFO @ Sat, 03 Apr 2021 08:34:50: 16000000 INFO @ Sat, 03 Apr 2021 08:34:50: 12000000 INFO @ Sat, 03 Apr 2021 08:34:52: 21000000 INFO @ Sat, 03 Apr 2021 08:34:58: 17000000 INFO @ Sat, 03 Apr 2021 08:34:58: 13000000 INFO @ Sat, 03 Apr 2021 08:34:59: 22000000 INFO @ Sat, 03 Apr 2021 08:35:05: 18000000 INFO @ Sat, 03 Apr 2021 08:35:05: 14000000 INFO @ Sat, 03 Apr 2021 08:35:06: 23000000 INFO @ Sat, 03 Apr 2021 08:35:12: 19000000 INFO @ Sat, 03 Apr 2021 08:35:13: 15000000 INFO @ Sat, 03 Apr 2021 08:35:14: 24000000 INFO @ Sat, 03 Apr 2021 08:35:20: 20000000 INFO @ Sat, 03 Apr 2021 08:35:20: 16000000 INFO @ Sat, 03 Apr 2021 08:35:21: 25000000 INFO @ Sat, 03 Apr 2021 08:35:27: 21000000 INFO @ Sat, 03 Apr 2021 08:35:27: 17000000 INFO @ Sat, 03 Apr 2021 08:35:28: 26000000 INFO @ Sat, 03 Apr 2021 08:35:35: 22000000 INFO @ Sat, 03 Apr 2021 08:35:35: 18000000 INFO @ Sat, 03 Apr 2021 08:35:35: 27000000 INFO @ Sat, 03 Apr 2021 08:35:42: 23000000 INFO @ Sat, 03 Apr 2021 08:35:42: 19000000 INFO @ Sat, 03 Apr 2021 08:35:42: 28000000 INFO @ Sat, 03 Apr 2021 08:35:49: 24000000 INFO @ Sat, 03 Apr 2021 08:35:49: 20000000 INFO @ Sat, 03 Apr 2021 08:35:49: 29000000 INFO @ Sat, 03 Apr 2021 08:35:56: 25000000 INFO @ Sat, 03 Apr 2021 08:35:57: 21000000 INFO @ Sat, 03 Apr 2021 08:35:57: 30000000 INFO @ Sat, 03 Apr 2021 08:36:03: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:36:04: 22000000 INFO @ Sat, 03 Apr 2021 08:36:04: 31000000 INFO @ Sat, 03 Apr 2021 08:36:11: 27000000 INFO @ Sat, 03 Apr 2021 08:36:12: 23000000 INFO @ Sat, 03 Apr 2021 08:36:12: 32000000 INFO @ Sat, 03 Apr 2021 08:36:18: 28000000 INFO @ Sat, 03 Apr 2021 08:36:19: 24000000 INFO @ Sat, 03 Apr 2021 08:36:20: 33000000 INFO @ Sat, 03 Apr 2021 08:36:26: 29000000 INFO @ Sat, 03 Apr 2021 08:36:26: 25000000 INFO @ Sat, 03 Apr 2021 08:36:28: 34000000 INFO @ Sat, 03 Apr 2021 08:36:34: 30000000 INFO @ Sat, 03 Apr 2021 08:36:34: 26000000 INFO @ Sat, 03 Apr 2021 08:36:35: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:36:35: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:36:35: #1 total tags in treatment: 13426652 INFO @ Sat, 03 Apr 2021 08:36:35: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:36:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:36:35: #1 tags after filtering in treatment: 10611940 INFO @ Sat, 03 Apr 2021 08:36:35: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 03 Apr 2021 08:36:35: #1 finished! INFO @ Sat, 03 Apr 2021 08:36:35: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:36:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:36:36: #2 number of paired peaks: 322 WARNING @ Sat, 03 Apr 2021 08:36:36: Fewer paired peaks (322) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 322 pairs to build model! INFO @ Sat, 03 Apr 2021 08:36:36: start model_add_line... INFO @ Sat, 03 Apr 2021 08:36:36: start X-correlation... INFO @ Sat, 03 Apr 2021 08:36:36: end of X-cor INFO @ Sat, 03 Apr 2021 08:36:36: #2 finished! INFO @ Sat, 03 Apr 2021 08:36:36: #2 predicted fragment length is 85 bps INFO @ Sat, 03 Apr 2021 08:36:36: #2 alternative fragment length(s) may be 4,85 bps INFO @ Sat, 03 Apr 2021 08:36:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277030/SRX7277030.05_model.r WARNING @ Sat, 03 Apr 2021 08:36:36: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:36:36: #2 You may need to consider one of the other alternative d(s): 4,85 WARNING @ Sat, 03 Apr 2021 08:36:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:36:36: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:36:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:36:41: 27000000 INFO @ Sat, 03 Apr 2021 08:36:41: 31000000 INFO @ Sat, 03 Apr 2021 08:36:48: 28000000 INFO @ Sat, 03 Apr 2021 08:36:48: 32000000 INFO @ Sat, 03 Apr 2021 08:36:56: 29000000 INFO @ Sat, 03 Apr 2021 08:36:56: 33000000 INFO @ Sat, 03 Apr 2021 08:37:02: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:37:03: 30000000 INFO @ Sat, 03 Apr 2021 08:37:03: 34000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:37:10: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:37:10: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:37:10: #1 total tags in treatment: 13426652 INFO @ Sat, 03 Apr 2021 08:37:10: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:37:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:37:10: 31000000 INFO @ Sat, 03 Apr 2021 08:37:10: #1 tags after filtering in treatment: 10611940 INFO @ Sat, 03 Apr 2021 08:37:10: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 03 Apr 2021 08:37:10: #1 finished! INFO @ Sat, 03 Apr 2021 08:37:10: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:37:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:37:11: #2 number of paired peaks: 322 WARNING @ Sat, 03 Apr 2021 08:37:11: Fewer paired peaks (322) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 322 pairs to build model! INFO @ Sat, 03 Apr 2021 08:37:11: start model_add_line... INFO @ Sat, 03 Apr 2021 08:37:11: start X-correlation... INFO @ Sat, 03 Apr 2021 08:37:11: end of X-cor INFO @ Sat, 03 Apr 2021 08:37:11: #2 finished! INFO @ Sat, 03 Apr 2021 08:37:11: #2 predicted fragment length is 85 bps INFO @ Sat, 03 Apr 2021 08:37:11: #2 alternative fragment length(s) may be 4,85 bps INFO @ Sat, 03 Apr 2021 08:37:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277030/SRX7277030.10_model.r WARNING @ Sat, 03 Apr 2021 08:37:11: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:37:11: #2 You may need to consider one of the other alternative d(s): 4,85 WARNING @ Sat, 03 Apr 2021 08:37:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:37:11: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:37:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:37:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277030/SRX7277030.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:37:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277030/SRX7277030.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:37:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277030/SRX7277030.05_summits.bed INFO @ Sat, 03 Apr 2021 08:37:15: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7994 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:37:17: 32000000 INFO @ Sat, 03 Apr 2021 08:37:24: 33000000 INFO @ Sat, 03 Apr 2021 08:37:31: 34000000 INFO @ Sat, 03 Apr 2021 08:37:36: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:37:37: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:37:37: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:37:37: #1 total tags in treatment: 13426652 INFO @ Sat, 03 Apr 2021 08:37:37: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:37:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:37:38: #1 tags after filtering in treatment: 10611940 INFO @ Sat, 03 Apr 2021 08:37:38: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 03 Apr 2021 08:37:38: #1 finished! INFO @ Sat, 03 Apr 2021 08:37:38: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:37:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:37:38: #2 number of paired peaks: 322 WARNING @ Sat, 03 Apr 2021 08:37:38: Fewer paired peaks (322) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 322 pairs to build model! INFO @ Sat, 03 Apr 2021 08:37:38: start model_add_line... INFO @ Sat, 03 Apr 2021 08:37:38: start X-correlation... INFO @ Sat, 03 Apr 2021 08:37:38: end of X-cor INFO @ Sat, 03 Apr 2021 08:37:38: #2 finished! INFO @ Sat, 03 Apr 2021 08:37:38: #2 predicted fragment length is 85 bps INFO @ Sat, 03 Apr 2021 08:37:38: #2 alternative fragment length(s) may be 4,85 bps INFO @ Sat, 03 Apr 2021 08:37:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277030/SRX7277030.20_model.r WARNING @ Sat, 03 Apr 2021 08:37:38: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:37:38: #2 You may need to consider one of the other alternative d(s): 4,85 WARNING @ Sat, 03 Apr 2021 08:37:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:37:38: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:37:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:37:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277030/SRX7277030.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:37:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277030/SRX7277030.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:37:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277030/SRX7277030.10_summits.bed INFO @ Sat, 03 Apr 2021 08:37:48: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2331 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:38:02: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:38:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277030/SRX7277030.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:38:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277030/SRX7277030.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:38:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277030/SRX7277030.20_summits.bed INFO @ Sat, 03 Apr 2021 08:38:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (150 records, 4 fields): 1 millis CompletedMACS2peakCalling