Job ID = 12265248 SRX = SRX4664627 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 24651194 spots for SRR7813054/SRR7813054.sra Written 24651194 spots for SRR7813054/SRR7813054.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265578 ("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: 00:51:59 24651194 reads; of these: 24651194 (100.00%) were paired; of these: 7580203 (30.75%) aligned concordantly 0 times 8414319 (34.13%) aligned concordantly exactly 1 time 8656672 (35.12%) aligned concordantly >1 times ---- 7580203 pairs aligned concordantly 0 times; of these: 2363870 (31.18%) aligned discordantly 1 time ---- 5216333 pairs aligned 0 times concordantly or discordantly; of these: 10432666 mates make up the pairs; of these: 6665326 (63.89%) aligned 0 times 865646 (8.30%) aligned exactly 1 time 2901694 (27.81%) aligned >1 times 86.48% overall alignment rate Time searching: 00:51:59 Overall time: 00:51:59 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] 4778677 / 19100216 = 0.2502 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 07:23:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4664627/SRX4664627.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4664627/SRX4664627.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4664627/SRX4664627.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4664627/SRX4664627.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 07:23:23: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:23:23: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:23:29: 1000000 INFO @ Sat, 03 Apr 2021 07:23:35: 2000000 INFO @ Sat, 03 Apr 2021 07:23:40: 3000000 INFO @ Sat, 03 Apr 2021 07:23:46: 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 07:23:52: 5000000 INFO @ Sat, 03 Apr 2021 07:23:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4664627/SRX4664627.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4664627/SRX4664627.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4664627/SRX4664627.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4664627/SRX4664627.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 07:23:53: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:23:53: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:23:58: 6000000 INFO @ Sat, 03 Apr 2021 07:23:59: 1000000 INFO @ Sat, 03 Apr 2021 07:24:03: 7000000 INFO @ Sat, 03 Apr 2021 07:24:05: 2000000 INFO @ Sat, 03 Apr 2021 07:24:09: 8000000 INFO @ Sat, 03 Apr 2021 07:24:11: 3000000 INFO @ Sat, 03 Apr 2021 07:24:15: 9000000 INFO @ Sat, 03 Apr 2021 07:24:17: 4000000 INFO @ Sat, 03 Apr 2021 07:24:20: 10000000 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 07:24:23: 5000000 INFO @ Sat, 03 Apr 2021 07:24:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4664627/SRX4664627.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4664627/SRX4664627.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4664627/SRX4664627.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4664627/SRX4664627.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 07:24:23: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:24:23: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:24:26: 11000000 INFO @ Sat, 03 Apr 2021 07:24:29: 6000000 INFO @ Sat, 03 Apr 2021 07:24:29: 1000000 INFO @ Sat, 03 Apr 2021 07:24:33: 12000000 INFO @ Sat, 03 Apr 2021 07:24:35: 7000000 INFO @ Sat, 03 Apr 2021 07:24:36: 2000000 INFO @ Sat, 03 Apr 2021 07:24:39: 13000000 INFO @ Sat, 03 Apr 2021 07:24:40: 8000000 INFO @ Sat, 03 Apr 2021 07:24:42: 3000000 INFO @ Sat, 03 Apr 2021 07:24:45: 14000000 INFO @ Sat, 03 Apr 2021 07:24:46: 9000000 INFO @ Sat, 03 Apr 2021 07:24:49: 4000000 INFO @ Sat, 03 Apr 2021 07:24:52: 15000000 INFO @ Sat, 03 Apr 2021 07:24:52: 10000000 INFO @ Sat, 03 Apr 2021 07:24:55: 5000000 INFO @ Sat, 03 Apr 2021 07:24:58: 11000000 INFO @ Sat, 03 Apr 2021 07:24:58: 16000000 INFO @ Sat, 03 Apr 2021 07:25:01: 6000000 INFO @ Sat, 03 Apr 2021 07:25:05: 17000000 INFO @ Sat, 03 Apr 2021 07:25:05: 12000000 INFO @ Sat, 03 Apr 2021 07:25:08: 7000000 INFO @ Sat, 03 Apr 2021 07:25:11: 13000000 INFO @ Sat, 03 Apr 2021 07:25:11: 18000000 INFO @ Sat, 03 Apr 2021 07:25:14: 8000000 INFO @ Sat, 03 Apr 2021 07:25:16: 14000000 INFO @ Sat, 03 Apr 2021 07:25:17: 19000000 INFO @ Sat, 03 Apr 2021 07:25:20: 9000000 INFO @ Sat, 03 Apr 2021 07:25:22: 15000000 INFO @ Sat, 03 Apr 2021 07:25:23: 20000000 INFO @ Sat, 03 Apr 2021 07:25:26: 10000000 INFO @ Sat, 03 Apr 2021 07:25:28: 16000000 INFO @ Sat, 03 Apr 2021 07:25:30: 21000000 INFO @ Sat, 03 Apr 2021 07:25:33: 11000000 INFO @ Sat, 03 Apr 2021 07:25:34: 17000000 INFO @ Sat, 03 Apr 2021 07:25:36: 22000000 INFO @ Sat, 03 Apr 2021 07:25:39: 12000000 INFO @ Sat, 03 Apr 2021 07:25:40: 18000000 INFO @ Sat, 03 Apr 2021 07:25:42: 23000000 INFO @ Sat, 03 Apr 2021 07:25:45: 13000000 INFO @ Sat, 03 Apr 2021 07:25:46: 19000000 INFO @ Sat, 03 Apr 2021 07:25:48: 24000000 INFO @ Sat, 03 Apr 2021 07:25:52: 14000000 INFO @ Sat, 03 Apr 2021 07:25:53: 20000000 INFO @ Sat, 03 Apr 2021 07:25:54: 25000000 INFO @ Sat, 03 Apr 2021 07:25:58: 15000000 INFO @ Sat, 03 Apr 2021 07:25:59: 21000000 INFO @ Sat, 03 Apr 2021 07:26:00: 26000000 INFO @ Sat, 03 Apr 2021 07:26:04: 22000000 INFO @ Sat, 03 Apr 2021 07:26:04: 16000000 INFO @ Sat, 03 Apr 2021 07:26:06: 27000000 INFO @ Sat, 03 Apr 2021 07:26:10: 23000000 INFO @ Sat, 03 Apr 2021 07:26:11: 17000000 INFO @ Sat, 03 Apr 2021 07:26:12: 28000000 INFO @ Sat, 03 Apr 2021 07:26:16: 24000000 INFO @ Sat, 03 Apr 2021 07:26:17: 18000000 INFO @ Sat, 03 Apr 2021 07:26:19: 29000000 INFO @ Sat, 03 Apr 2021 07:26:21: 25000000 INFO @ Sat, 03 Apr 2021 07:26:23: 19000000 INFO @ Sat, 03 Apr 2021 07:26:25: 30000000 INFO @ Sat, 03 Apr 2021 07:26:27: 26000000 INFO @ Sat, 03 Apr 2021 07:26:29: 20000000 INFO @ Sat, 03 Apr 2021 07:26:31: 31000000 INFO @ Sat, 03 Apr 2021 07:26:33: 27000000 INFO @ Sat, 03 Apr 2021 07:26:36: 21000000 INFO @ Sat, 03 Apr 2021 07:26:38: 32000000 INFO @ Sat, 03 Apr 2021 07:26:39: 28000000 INFO @ Sat, 03 Apr 2021 07:26:41: 22000000 INFO @ Sat, 03 Apr 2021 07:26:44: 33000000 INFO @ Sat, 03 Apr 2021 07:26:44: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:26:44: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:26:44: #1 total tags in treatment: 12537080 INFO @ Sat, 03 Apr 2021 07:26:44: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:26:44: #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 07:26:45: #1 tags after filtering in treatment: 9842729 INFO @ Sat, 03 Apr 2021 07:26:45: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 03 Apr 2021 07:26:45: #1 finished! INFO @ Sat, 03 Apr 2021 07:26:45: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:26:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:26:45: 29000000 INFO @ Sat, 03 Apr 2021 07:26:45: #2 number of paired peaks: 803 WARNING @ Sat, 03 Apr 2021 07:26:45: Fewer paired peaks (803) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 803 pairs to build model! INFO @ Sat, 03 Apr 2021 07:26:45: start model_add_line... INFO @ Sat, 03 Apr 2021 07:26:45: start X-correlation... INFO @ Sat, 03 Apr 2021 07:26:45: end of X-cor INFO @ Sat, 03 Apr 2021 07:26:45: #2 finished! INFO @ Sat, 03 Apr 2021 07:26:45: #2 predicted fragment length is 75 bps INFO @ Sat, 03 Apr 2021 07:26:45: #2 alternative fragment length(s) may be 4,75 bps INFO @ Sat, 03 Apr 2021 07:26:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4664627/SRX4664627.05_model.r WARNING @ Sat, 03 Apr 2021 07:26:45: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:26:45: #2 You may need to consider one of the other alternative d(s): 4,75 WARNING @ Sat, 03 Apr 2021 07:26:45: #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 07:26:45: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:26:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:26:47: 23000000 INFO @ Sat, 03 Apr 2021 07:26:51: 30000000 INFO @ Sat, 03 Apr 2021 07:26:52: 24000000 INFO @ Sat, 03 Apr 2021 07:26:57: 31000000 INFO @ Sat, 03 Apr 2021 07:26:58: 25000000 INFO @ Sat, 03 Apr 2021 07:27:03: 32000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:27:03: 26000000 INFO @ Sat, 03 Apr 2021 07:27:04: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:27:09: 33000000 INFO @ Sat, 03 Apr 2021 07:27:09: 27000000 INFO @ Sat, 03 Apr 2021 07:27:09: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:27:09: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:27:09: #1 total tags in treatment: 12537080 INFO @ Sat, 03 Apr 2021 07:27:09: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:27:09: #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 07:27:10: #1 tags after filtering in treatment: 9842729 INFO @ Sat, 03 Apr 2021 07:27:10: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 03 Apr 2021 07:27:10: #1 finished! INFO @ Sat, 03 Apr 2021 07:27:10: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:27:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:27:10: #2 number of paired peaks: 803 WARNING @ Sat, 03 Apr 2021 07:27:10: Fewer paired peaks (803) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 803 pairs to build model! INFO @ Sat, 03 Apr 2021 07:27:10: start model_add_line... INFO @ Sat, 03 Apr 2021 07:27:11: start X-correlation... INFO @ Sat, 03 Apr 2021 07:27:11: end of X-cor INFO @ Sat, 03 Apr 2021 07:27:11: #2 finished! INFO @ Sat, 03 Apr 2021 07:27:11: #2 predicted fragment length is 75 bps INFO @ Sat, 03 Apr 2021 07:27:11: #2 alternative fragment length(s) may be 4,75 bps INFO @ Sat, 03 Apr 2021 07:27:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4664627/SRX4664627.10_model.r WARNING @ Sat, 03 Apr 2021 07:27:11: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:27:11: #2 You may need to consider one of the other alternative d(s): 4,75 WARNING @ Sat, 03 Apr 2021 07:27:11: #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 07:27:11: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:27:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:27:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4664627/SRX4664627.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:27:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4664627/SRX4664627.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:27:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4664627/SRX4664627.05_summits.bed INFO @ Sat, 03 Apr 2021 07:27:13: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5069 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:27:15: 28000000 INFO @ Sat, 03 Apr 2021 07:27:20: 29000000 INFO @ Sat, 03 Apr 2021 07:27:26: 30000000 INFO @ Sat, 03 Apr 2021 07:27:29: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:27:31: 31000000 INFO @ Sat, 03 Apr 2021 07:27:37: 32000000 INFO @ Sat, 03 Apr 2021 07:27:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4664627/SRX4664627.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:27:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4664627/SRX4664627.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:27:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4664627/SRX4664627.10_summits.bed INFO @ Sat, 03 Apr 2021 07:27:39: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2375 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:27:42: 33000000 INFO @ Sat, 03 Apr 2021 07:27:43: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:27:43: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:27:43: #1 total tags in treatment: 12537080 INFO @ Sat, 03 Apr 2021 07:27:43: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:27:43: #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 07:27:43: #1 tags after filtering in treatment: 9842729 INFO @ Sat, 03 Apr 2021 07:27:43: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 03 Apr 2021 07:27:43: #1 finished! INFO @ Sat, 03 Apr 2021 07:27:43: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:27:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:27:44: #2 number of paired peaks: 803 WARNING @ Sat, 03 Apr 2021 07:27:44: Fewer paired peaks (803) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 803 pairs to build model! INFO @ Sat, 03 Apr 2021 07:27:44: start model_add_line... INFO @ Sat, 03 Apr 2021 07:27:44: start X-correlation... INFO @ Sat, 03 Apr 2021 07:27:44: end of X-cor INFO @ Sat, 03 Apr 2021 07:27:44: #2 finished! INFO @ Sat, 03 Apr 2021 07:27:44: #2 predicted fragment length is 75 bps INFO @ Sat, 03 Apr 2021 07:27:44: #2 alternative fragment length(s) may be 4,75 bps INFO @ Sat, 03 Apr 2021 07:27:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4664627/SRX4664627.20_model.r WARNING @ Sat, 03 Apr 2021 07:27:44: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:27:44: #2 You may need to consider one of the other alternative d(s): 4,75 WARNING @ Sat, 03 Apr 2021 07:27:44: #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 07:27:44: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:27:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:28:02: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:28:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4664627/SRX4664627.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:28:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4664627/SRX4664627.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:28:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4664627/SRX4664627.20_summits.bed INFO @ Sat, 03 Apr 2021 07:28:11: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (806 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。