Job ID = 14168947 SRX = SRX9910782 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 38889260 spots for SRR13498853/SRR13498853.sra Written 38889260 spots for SRR13498853/SRR13498853.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170096 ("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: 01:27:30 38889260 reads; of these: 38889260 (100.00%) were paired; of these: 14761828 (37.96%) aligned concordantly 0 times 13227856 (34.01%) aligned concordantly exactly 1 time 10899576 (28.03%) aligned concordantly >1 times ---- 14761828 pairs aligned concordantly 0 times; of these: 1789047 (12.12%) aligned discordantly 1 time ---- 12972781 pairs aligned 0 times concordantly or discordantly; of these: 25945562 mates make up the pairs; of these: 20115167 (77.53%) aligned 0 times 482221 (1.86%) aligned exactly 1 time 5348174 (20.61%) aligned >1 times 74.14% overall alignment rate Time searching: 01:27:30 Overall time: 01:27:30 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 44 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] 12765004 / 25724365 = 0.4962 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 @ Fri, 10 Dec 2021 23:54:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9910782/SRX9910782.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9910782/SRX9910782.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9910782/SRX9910782.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9910782/SRX9910782.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 @ Fri, 10 Dec 2021 23:54:00: #1 read tag files... INFO @ Fri, 10 Dec 2021 23:54:00: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 23:54:09: 1000000 INFO @ Fri, 10 Dec 2021 23:54:19: 2000000 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 @ Fri, 10 Dec 2021 23:54:28: 3000000 INFO @ Fri, 10 Dec 2021 23:54:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9910782/SRX9910782.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9910782/SRX9910782.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9910782/SRX9910782.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9910782/SRX9910782.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 @ Fri, 10 Dec 2021 23:54:29: #1 read tag files... INFO @ Fri, 10 Dec 2021 23:54:29: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 23:54:38: 4000000 INFO @ Fri, 10 Dec 2021 23:54:39: 1000000 INFO @ Fri, 10 Dec 2021 23:54:47: 5000000 INFO @ Fri, 10 Dec 2021 23:54:48: 2000000 INFO @ Fri, 10 Dec 2021 23:54:57: 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 @ Fri, 10 Dec 2021 23:54:58: 3000000 INFO @ Fri, 10 Dec 2021 23:54:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9910782/SRX9910782.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9910782/SRX9910782.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9910782/SRX9910782.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9910782/SRX9910782.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 @ Fri, 10 Dec 2021 23:54:59: #1 read tag files... INFO @ Fri, 10 Dec 2021 23:54:59: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 23:55:07: 7000000 INFO @ Fri, 10 Dec 2021 23:55:08: 4000000 INFO @ Fri, 10 Dec 2021 23:55:09: 1000000 INFO @ Fri, 10 Dec 2021 23:55:18: 8000000 INFO @ Fri, 10 Dec 2021 23:55:19: 5000000 INFO @ Fri, 10 Dec 2021 23:55:20: 2000000 INFO @ Fri, 10 Dec 2021 23:55:28: 9000000 INFO @ Fri, 10 Dec 2021 23:55:29: 6000000 INFO @ Fri, 10 Dec 2021 23:55:30: 3000000 INFO @ Fri, 10 Dec 2021 23:55:38: 10000000 INFO @ Fri, 10 Dec 2021 23:55:39: 7000000 INFO @ Fri, 10 Dec 2021 23:55:41: 4000000 INFO @ Fri, 10 Dec 2021 23:55:48: 11000000 INFO @ Fri, 10 Dec 2021 23:55:50: 8000000 INFO @ Fri, 10 Dec 2021 23:55:51: 5000000 INFO @ Fri, 10 Dec 2021 23:55:58: 12000000 INFO @ Fri, 10 Dec 2021 23:56:00: 9000000 INFO @ Fri, 10 Dec 2021 23:56:01: 6000000 INFO @ Fri, 10 Dec 2021 23:56:08: 13000000 INFO @ Fri, 10 Dec 2021 23:56:10: 10000000 INFO @ Fri, 10 Dec 2021 23:56:12: 7000000 INFO @ Fri, 10 Dec 2021 23:56:18: 14000000 INFO @ Fri, 10 Dec 2021 23:56:20: 11000000 INFO @ Fri, 10 Dec 2021 23:56:22: 8000000 INFO @ Fri, 10 Dec 2021 23:56:28: 15000000 INFO @ Fri, 10 Dec 2021 23:56:30: 12000000 INFO @ Fri, 10 Dec 2021 23:56:33: 9000000 INFO @ Fri, 10 Dec 2021 23:56:39: 16000000 INFO @ Fri, 10 Dec 2021 23:56:40: 13000000 INFO @ Fri, 10 Dec 2021 23:56:43: 10000000 INFO @ Fri, 10 Dec 2021 23:56:49: 17000000 INFO @ Fri, 10 Dec 2021 23:56:50: 14000000 INFO @ Fri, 10 Dec 2021 23:56:53: 11000000 INFO @ Fri, 10 Dec 2021 23:56:59: 18000000 INFO @ Fri, 10 Dec 2021 23:57:00: 15000000 INFO @ Fri, 10 Dec 2021 23:57:03: 12000000 INFO @ Fri, 10 Dec 2021 23:57:09: 19000000 INFO @ Fri, 10 Dec 2021 23:57:10: 16000000 INFO @ Fri, 10 Dec 2021 23:57:13: 13000000 INFO @ Fri, 10 Dec 2021 23:57:18: 20000000 INFO @ Fri, 10 Dec 2021 23:57:20: 17000000 INFO @ Fri, 10 Dec 2021 23:57:23: 14000000 INFO @ Fri, 10 Dec 2021 23:57:28: 21000000 INFO @ Fri, 10 Dec 2021 23:57:30: 18000000 INFO @ Fri, 10 Dec 2021 23:57:33: 15000000 INFO @ Fri, 10 Dec 2021 23:57:38: 22000000 INFO @ Fri, 10 Dec 2021 23:57:40: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 23:57:43: 16000000 INFO @ Fri, 10 Dec 2021 23:57:48: 23000000 INFO @ Fri, 10 Dec 2021 23:57:50: 20000000 INFO @ Fri, 10 Dec 2021 23:57:53: 17000000 INFO @ Fri, 10 Dec 2021 23:57:58: 24000000 INFO @ Fri, 10 Dec 2021 23:57:59: 21000000 INFO @ Fri, 10 Dec 2021 23:58:03: 18000000 INFO @ Fri, 10 Dec 2021 23:58:08: 25000000 INFO @ Fri, 10 Dec 2021 23:58:09: 22000000 INFO @ Fri, 10 Dec 2021 23:58:13: 19000000 INFO @ Fri, 10 Dec 2021 23:58:18: 26000000 INFO @ Fri, 10 Dec 2021 23:58:19: 23000000 INFO @ Fri, 10 Dec 2021 23:58:23: 20000000 INFO @ Fri, 10 Dec 2021 23:58:27: 27000000 INFO @ Fri, 10 Dec 2021 23:58:29: 24000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 23:58:32: 21000000 INFO @ Fri, 10 Dec 2021 23:58:37: 28000000 INFO @ Fri, 10 Dec 2021 23:58:39: 25000000 INFO @ Fri, 10 Dec 2021 23:58:42: 22000000 INFO @ Fri, 10 Dec 2021 23:58:47: 29000000 INFO @ Fri, 10 Dec 2021 23:58:48: 26000000 INFO @ Fri, 10 Dec 2021 23:58:52: 23000000 INFO @ Fri, 10 Dec 2021 23:58:57: 30000000 INFO @ Fri, 10 Dec 2021 23:58:59: 27000000 INFO @ Fri, 10 Dec 2021 23:59:01: 24000000 INFO @ Fri, 10 Dec 2021 23:59:07: 31000000 INFO @ Fri, 10 Dec 2021 23:59:08: 28000000 INFO @ Fri, 10 Dec 2021 23:59:11: 25000000 INFO @ Fri, 10 Dec 2021 23:59:17: 32000000 INFO @ Fri, 10 Dec 2021 23:59:18: #1 tag size is determined as 151 bps INFO @ Fri, 10 Dec 2021 23:59:18: #1 tag size = 151 INFO @ Fri, 10 Dec 2021 23:59:18: #1 total tags in treatment: 11912961 INFO @ Fri, 10 Dec 2021 23:59:18: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 23:59:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 23:59:18: #1 tags after filtering in treatment: 9416290 INFO @ Fri, 10 Dec 2021 23:59:18: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 10 Dec 2021 23:59:18: #1 finished! INFO @ Fri, 10 Dec 2021 23:59:18: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 23:59:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 23:59:18: 29000000 INFO @ Fri, 10 Dec 2021 23:59:19: #2 number of paired peaks: 236 WARNING @ Fri, 10 Dec 2021 23:59:19: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Fri, 10 Dec 2021 23:59:19: start model_add_line... INFO @ Fri, 10 Dec 2021 23:59:19: start X-correlation... INFO @ Fri, 10 Dec 2021 23:59:19: end of X-cor INFO @ Fri, 10 Dec 2021 23:59:19: #2 finished! INFO @ Fri, 10 Dec 2021 23:59:19: #2 predicted fragment length is 201 bps INFO @ Fri, 10 Dec 2021 23:59:19: #2 alternative fragment length(s) may be 201 bps INFO @ Fri, 10 Dec 2021 23:59:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9910782/SRX9910782.05_model.r WARNING @ Fri, 10 Dec 2021 23:59:19: #2 Since the d (201) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 23:59:19: #2 You may need to consider one of the other alternative d(s): 201 WARNING @ Fri, 10 Dec 2021 23:59:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 23:59:19: #3 Call peaks... INFO @ Fri, 10 Dec 2021 23:59:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 23:59:21: 26000000 INFO @ Fri, 10 Dec 2021 23:59:28: 30000000 INFO @ Fri, 10 Dec 2021 23:59:31: 27000000 INFO @ Fri, 10 Dec 2021 23:59:38: 31000000 INFO @ Fri, 10 Dec 2021 23:59:38: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 23:59:41: 28000000 INFO @ Fri, 10 Dec 2021 23:59:47: 32000000 INFO @ Fri, 10 Dec 2021 23:59:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9910782/SRX9910782.05_peaks.xls INFO @ Fri, 10 Dec 2021 23:59:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9910782/SRX9910782.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 23:59:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9910782/SRX9910782.05_summits.bed INFO @ Fri, 10 Dec 2021 23:59:48: Done! INFO @ Fri, 10 Dec 2021 23:59:48: #1 tag size is determined as 151 bps INFO @ Fri, 10 Dec 2021 23:59:48: #1 tag size = 151 INFO @ Fri, 10 Dec 2021 23:59:48: #1 total tags in treatment: 11912961 INFO @ Fri, 10 Dec 2021 23:59:48: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 23:59:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3058 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 23:59:48: #1 tags after filtering in treatment: 9416290 INFO @ Fri, 10 Dec 2021 23:59:48: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 10 Dec 2021 23:59:48: #1 finished! INFO @ Fri, 10 Dec 2021 23:59:48: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 23:59:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 23:59:49: #2 number of paired peaks: 236 WARNING @ Fri, 10 Dec 2021 23:59:49: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Fri, 10 Dec 2021 23:59:49: start model_add_line... INFO @ Fri, 10 Dec 2021 23:59:49: start X-correlation... INFO @ Fri, 10 Dec 2021 23:59:49: end of X-cor INFO @ Fri, 10 Dec 2021 23:59:49: #2 finished! INFO @ Fri, 10 Dec 2021 23:59:49: #2 predicted fragment length is 201 bps INFO @ Fri, 10 Dec 2021 23:59:49: #2 alternative fragment length(s) may be 201 bps INFO @ Fri, 10 Dec 2021 23:59:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9910782/SRX9910782.10_model.r WARNING @ Fri, 10 Dec 2021 23:59:49: #2 Since the d (201) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 23:59:49: #2 You may need to consider one of the other alternative d(s): 201 WARNING @ Fri, 10 Dec 2021 23:59:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 23:59:49: #3 Call peaks... INFO @ Fri, 10 Dec 2021 23:59:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 23:59:51: 29000000 INFO @ Sat, 11 Dec 2021 00:00:00: 30000000 INFO @ Sat, 11 Dec 2021 00:00:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 00:00:10: 31000000 INFO @ Sat, 11 Dec 2021 00:00:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9910782/SRX9910782.10_peaks.xls INFO @ Sat, 11 Dec 2021 00:00:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9910782/SRX9910782.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 00:00:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9910782/SRX9910782.10_summits.bed INFO @ Sat, 11 Dec 2021 00:00:18: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (903 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 00:00:18: 32000000 INFO @ Sat, 11 Dec 2021 00:00:20: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 00:00:20: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 00:00:20: #1 total tags in treatment: 11912961 INFO @ Sat, 11 Dec 2021 00:00:20: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 00:00:20: #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 00:00:20: #1 tags after filtering in treatment: 9416290 INFO @ Sat, 11 Dec 2021 00:00:20: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 11 Dec 2021 00:00:20: #1 finished! INFO @ Sat, 11 Dec 2021 00:00:20: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 00:00:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 00:00:20: #2 number of paired peaks: 236 WARNING @ Sat, 11 Dec 2021 00:00:20: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Sat, 11 Dec 2021 00:00:20: start model_add_line... INFO @ Sat, 11 Dec 2021 00:00:21: start X-correlation... INFO @ Sat, 11 Dec 2021 00:00:21: end of X-cor INFO @ Sat, 11 Dec 2021 00:00:21: #2 finished! INFO @ Sat, 11 Dec 2021 00:00:21: #2 predicted fragment length is 201 bps INFO @ Sat, 11 Dec 2021 00:00:21: #2 alternative fragment length(s) may be 201 bps INFO @ Sat, 11 Dec 2021 00:00:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9910782/SRX9910782.20_model.r WARNING @ Sat, 11 Dec 2021 00:00:21: #2 Since the d (201) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 00:00:21: #2 You may need to consider one of the other alternative d(s): 201 WARNING @ Sat, 11 Dec 2021 00:00:21: #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 00:00:21: #3 Call peaks... INFO @ Sat, 11 Dec 2021 00:00:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 00:00:40: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 00:00:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9910782/SRX9910782.20_peaks.xls INFO @ Sat, 11 Dec 2021 00:00:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9910782/SRX9910782.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 00:00:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9910782/SRX9910782.20_summits.bed INFO @ Sat, 11 Dec 2021 00:00:49: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (296 records, 4 fields): 1 millis CompletedMACS2peakCalling