Job ID = 12265502 SRX = SRX7277010 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 20573638 spots for SRR10597275/SRR10597275.sra Written 20573638 spots for SRR10597275/SRR10597275.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265784 ("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: 00:40:05 20573638 reads; of these: 20573638 (100.00%) were paired; of these: 7775050 (37.79%) aligned concordantly 0 times 8464667 (41.14%) aligned concordantly exactly 1 time 4333921 (21.07%) aligned concordantly >1 times ---- 7775050 pairs aligned concordantly 0 times; of these: 2174821 (27.97%) aligned discordantly 1 time ---- 5600229 pairs aligned 0 times concordantly or discordantly; of these: 11200458 mates make up the pairs; of these: 8743415 (78.06%) aligned 0 times 604965 (5.40%) aligned exactly 1 time 1852078 (16.54%) aligned >1 times 78.75% overall alignment rate Time searching: 00:40:05 Overall time: 00:40:05 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] 2241280 / 14858451 = 0.1508 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 08:17:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277010/SRX7277010.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277010/SRX7277010.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277010/SRX7277010.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277010/SRX7277010.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 08:17:51: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:17:51: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:17:59: 1000000 INFO @ Sat, 03 Apr 2021 08:18:07: 2000000 INFO @ Sat, 03 Apr 2021 08:18:15: 3000000 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 08:18:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277010/SRX7277010.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277010/SRX7277010.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277010/SRX7277010.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277010/SRX7277010.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 08:18:21: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:18:21: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:18:23: 4000000 INFO @ Sat, 03 Apr 2021 08:18:31: 1000000 INFO @ Sat, 03 Apr 2021 08:18:32: 5000000 INFO @ Sat, 03 Apr 2021 08:18:40: 6000000 INFO @ Sat, 03 Apr 2021 08:18:41: 2000000 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 08:18:49: 7000000 INFO @ Sat, 03 Apr 2021 08:18:50: 3000000 INFO @ Sat, 03 Apr 2021 08:18:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277010/SRX7277010.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277010/SRX7277010.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277010/SRX7277010.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277010/SRX7277010.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 08:18:51: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:18:51: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:18:58: 8000000 INFO @ Sat, 03 Apr 2021 08:19:00: 4000000 INFO @ Sat, 03 Apr 2021 08:19:01: 1000000 INFO @ Sat, 03 Apr 2021 08:19:08: 9000000 INFO @ Sat, 03 Apr 2021 08:19:10: 5000000 INFO @ Sat, 03 Apr 2021 08:19:11: 2000000 INFO @ Sat, 03 Apr 2021 08:19:18: 10000000 INFO @ Sat, 03 Apr 2021 08:19:20: 6000000 INFO @ Sat, 03 Apr 2021 08:19:20: 3000000 INFO @ Sat, 03 Apr 2021 08:19:27: 11000000 INFO @ Sat, 03 Apr 2021 08:19:29: 7000000 INFO @ Sat, 03 Apr 2021 08:19:30: 4000000 INFO @ Sat, 03 Apr 2021 08:19:37: 12000000 INFO @ Sat, 03 Apr 2021 08:19:39: 8000000 INFO @ Sat, 03 Apr 2021 08:19:39: 5000000 INFO @ Sat, 03 Apr 2021 08:19:46: 13000000 INFO @ Sat, 03 Apr 2021 08:19:48: 9000000 INFO @ Sat, 03 Apr 2021 08:19:49: 6000000 INFO @ Sat, 03 Apr 2021 08:19:56: 14000000 INFO @ Sat, 03 Apr 2021 08:19:58: 10000000 INFO @ Sat, 03 Apr 2021 08:19:58: 7000000 INFO @ Sat, 03 Apr 2021 08:20:05: 15000000 INFO @ Sat, 03 Apr 2021 08:20:08: 11000000 INFO @ Sat, 03 Apr 2021 08:20:08: 8000000 INFO @ Sat, 03 Apr 2021 08:20:15: 16000000 INFO @ Sat, 03 Apr 2021 08:20:17: 12000000 INFO @ Sat, 03 Apr 2021 08:20:18: 9000000 INFO @ Sat, 03 Apr 2021 08:20:24: 17000000 INFO @ Sat, 03 Apr 2021 08:20:27: 13000000 INFO @ Sat, 03 Apr 2021 08:20:27: 10000000 INFO @ Sat, 03 Apr 2021 08:20:34: 18000000 INFO @ Sat, 03 Apr 2021 08:20:36: 14000000 INFO @ Sat, 03 Apr 2021 08:20:37: 11000000 INFO @ Sat, 03 Apr 2021 08:20:43: 19000000 INFO @ Sat, 03 Apr 2021 08:20:46: 12000000 INFO @ Sat, 03 Apr 2021 08:20:46: 15000000 INFO @ Sat, 03 Apr 2021 08:20:52: 20000000 INFO @ Sat, 03 Apr 2021 08:20:55: 13000000 INFO @ Sat, 03 Apr 2021 08:20:56: 16000000 INFO @ Sat, 03 Apr 2021 08:21:01: 21000000 INFO @ Sat, 03 Apr 2021 08:21:04: 14000000 INFO @ Sat, 03 Apr 2021 08:21:05: 17000000 INFO @ Sat, 03 Apr 2021 08:21:10: 22000000 INFO @ Sat, 03 Apr 2021 08:21:13: 15000000 INFO @ Sat, 03 Apr 2021 08:21:15: 18000000 INFO @ Sat, 03 Apr 2021 08:21:19: 23000000 INFO @ Sat, 03 Apr 2021 08:21:23: 16000000 INFO @ Sat, 03 Apr 2021 08:21:24: 19000000 INFO @ Sat, 03 Apr 2021 08:21:29: 24000000 INFO @ Sat, 03 Apr 2021 08:21:32: 17000000 INFO @ Sat, 03 Apr 2021 08:21:34: 20000000 INFO @ Sat, 03 Apr 2021 08:21:38: 25000000 INFO @ Sat, 03 Apr 2021 08:21:42: 18000000 INFO @ Sat, 03 Apr 2021 08:21:43: 21000000 INFO @ Sat, 03 Apr 2021 08:21:47: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:21:52: 22000000 INFO @ Sat, 03 Apr 2021 08:21:53: 19000000 INFO @ Sat, 03 Apr 2021 08:21:56: 27000000 INFO @ Sat, 03 Apr 2021 08:22:01: 20000000 INFO @ Sat, 03 Apr 2021 08:22:02: 23000000 INFO @ Sat, 03 Apr 2021 08:22:05: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:22:05: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:22:05: #1 total tags in treatment: 10635115 INFO @ Sat, 03 Apr 2021 08:22:05: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:22:05: #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 08:22:05: #1 tags after filtering in treatment: 8753048 INFO @ Sat, 03 Apr 2021 08:22:05: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 03 Apr 2021 08:22:05: #1 finished! INFO @ Sat, 03 Apr 2021 08:22:05: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:22:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:22:06: #2 number of paired peaks: 122 WARNING @ Sat, 03 Apr 2021 08:22:06: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Sat, 03 Apr 2021 08:22:06: start model_add_line... INFO @ Sat, 03 Apr 2021 08:22:06: start X-correlation... INFO @ Sat, 03 Apr 2021 08:22:06: end of X-cor INFO @ Sat, 03 Apr 2021 08:22:06: #2 finished! INFO @ Sat, 03 Apr 2021 08:22:06: #2 predicted fragment length is 146 bps INFO @ Sat, 03 Apr 2021 08:22:06: #2 alternative fragment length(s) may be 3,106,124,146,560,584 bps INFO @ Sat, 03 Apr 2021 08:22:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277010/SRX7277010.05_model.r WARNING @ Sat, 03 Apr 2021 08:22:06: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:22:06: #2 You may need to consider one of the other alternative d(s): 3,106,124,146,560,584 WARNING @ Sat, 03 Apr 2021 08:22:06: #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 08:22:06: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:22:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:22:10: 21000000 INFO @ Sat, 03 Apr 2021 08:22:12: 24000000 INFO @ Sat, 03 Apr 2021 08:22:17: 22000000 INFO @ Sat, 03 Apr 2021 08:22:21: 25000000 INFO @ Sat, 03 Apr 2021 08:22:25: 23000000 INFO @ Sat, 03 Apr 2021 08:22:31: 26000000 INFO @ Sat, 03 Apr 2021 08:22:32: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:22:34: 24000000 INFO @ Sat, 03 Apr 2021 08:22:40: 27000000 INFO @ Sat, 03 Apr 2021 08:22:42: 25000000 INFO @ Sat, 03 Apr 2021 08:22:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277010/SRX7277010.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:22:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277010/SRX7277010.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:22:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277010/SRX7277010.05_summits.bed INFO @ Sat, 03 Apr 2021 08:22:46: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4136 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:22:49: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:22:49: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:22:49: #1 total tags in treatment: 10635115 INFO @ Sat, 03 Apr 2021 08:22:49: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:22:49: #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 08:22:49: #1 tags after filtering in treatment: 8753048 INFO @ Sat, 03 Apr 2021 08:22:49: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 03 Apr 2021 08:22:49: #1 finished! INFO @ Sat, 03 Apr 2021 08:22:49: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:22:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:22:50: #2 number of paired peaks: 122 WARNING @ Sat, 03 Apr 2021 08:22:50: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Sat, 03 Apr 2021 08:22:50: start model_add_line... INFO @ Sat, 03 Apr 2021 08:22:50: 26000000 INFO @ Sat, 03 Apr 2021 08:22:50: start X-correlation... INFO @ Sat, 03 Apr 2021 08:22:50: end of X-cor INFO @ Sat, 03 Apr 2021 08:22:50: #2 finished! INFO @ Sat, 03 Apr 2021 08:22:50: #2 predicted fragment length is 146 bps INFO @ Sat, 03 Apr 2021 08:22:50: #2 alternative fragment length(s) may be 3,106,124,146,560,584 bps INFO @ Sat, 03 Apr 2021 08:22:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277010/SRX7277010.10_model.r WARNING @ Sat, 03 Apr 2021 08:22:50: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:22:50: #2 You may need to consider one of the other alternative d(s): 3,106,124,146,560,584 WARNING @ Sat, 03 Apr 2021 08:22:50: #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 08:22:50: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:22:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:22:57: 27000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:23:04: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:23:04: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:23:04: #1 total tags in treatment: 10635115 INFO @ Sat, 03 Apr 2021 08:23:04: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:23:04: #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 08:23:05: #1 tags after filtering in treatment: 8753048 INFO @ Sat, 03 Apr 2021 08:23:05: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 03 Apr 2021 08:23:05: #1 finished! INFO @ Sat, 03 Apr 2021 08:23:05: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:23:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:23:05: #2 number of paired peaks: 122 WARNING @ Sat, 03 Apr 2021 08:23:05: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Sat, 03 Apr 2021 08:23:05: start model_add_line... INFO @ Sat, 03 Apr 2021 08:23:06: start X-correlation... INFO @ Sat, 03 Apr 2021 08:23:06: end of X-cor INFO @ Sat, 03 Apr 2021 08:23:06: #2 finished! INFO @ Sat, 03 Apr 2021 08:23:06: #2 predicted fragment length is 146 bps INFO @ Sat, 03 Apr 2021 08:23:06: #2 alternative fragment length(s) may be 3,106,124,146,560,584 bps INFO @ Sat, 03 Apr 2021 08:23:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277010/SRX7277010.20_model.r WARNING @ Sat, 03 Apr 2021 08:23:06: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:23:06: #2 You may need to consider one of the other alternative d(s): 3,106,124,146,560,584 WARNING @ Sat, 03 Apr 2021 08:23:06: #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 08:23:06: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:23:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:23:15: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:23:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277010/SRX7277010.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:23:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277010/SRX7277010.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:23:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277010/SRX7277010.10_summits.bed INFO @ Sat, 03 Apr 2021 08:23:29: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (847 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:23:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:23:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277010/SRX7277010.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:23:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277010/SRX7277010.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:23:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277010/SRX7277010.20_summits.bed INFO @ Sat, 03 Apr 2021 08:23:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (134 records, 4 fields): 2 millis CompletedMACS2peakCalling