Job ID = 6497353 SRX = SRX2011721 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T22:03:43 prefetch.2.10.7: 1) Downloading 'SRR4017963'... 2020-06-25T22:03:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:10:03 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:10:03 prefetch.2.10.7: 1) 'SRR4017963' was downloaded successfully Read 15974307 spots for SRR4017963/SRR4017963.sra Written 15974307 spots for SRR4017963/SRR4017963.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:25:28 15974307 reads; of these: 15974307 (100.00%) were paired; of these: 1694380 (10.61%) aligned concordantly 0 times 12342891 (77.27%) aligned concordantly exactly 1 time 1937036 (12.13%) aligned concordantly >1 times ---- 1694380 pairs aligned concordantly 0 times; of these: 1235411 (72.91%) aligned discordantly 1 time ---- 458969 pairs aligned 0 times concordantly or discordantly; of these: 917938 mates make up the pairs; of these: 318492 (34.70%) aligned 0 times 275685 (30.03%) aligned exactly 1 time 323761 (35.27%) aligned >1 times 99.00% overall alignment rate Time searching: 00:25:29 Overall time: 00:25:29 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 1955728 / 15357112 = 0.1273 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 07:51:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2011721/SRX2011721.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2011721/SRX2011721.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2011721/SRX2011721.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2011721/SRX2011721.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 26 Jun 2020 07:51:40: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:51:40: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:51:48: 1000000 INFO @ Fri, 26 Jun 2020 07:51:56: 2000000 INFO @ Fri, 26 Jun 2020 07:52:04: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 07:52:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2011721/SRX2011721.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2011721/SRX2011721.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2011721/SRX2011721.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2011721/SRX2011721.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 26 Jun 2020 07:52:10: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:52:10: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:52:12: 4000000 INFO @ Fri, 26 Jun 2020 07:52:19: 1000000 INFO @ Fri, 26 Jun 2020 07:52:21: 5000000 INFO @ Fri, 26 Jun 2020 07:52:28: 2000000 INFO @ Fri, 26 Jun 2020 07:52:30: 6000000 INFO @ Fri, 26 Jun 2020 07:52:37: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 07:52:39: 7000000 INFO @ Fri, 26 Jun 2020 07:52:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2011721/SRX2011721.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2011721/SRX2011721.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2011721/SRX2011721.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2011721/SRX2011721.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 26 Jun 2020 07:52:39: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:52:39: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:52:47: 4000000 INFO @ Fri, 26 Jun 2020 07:52:50: 8000000 INFO @ Fri, 26 Jun 2020 07:52:50: 1000000 INFO @ Fri, 26 Jun 2020 07:52:57: 5000000 INFO @ Fri, 26 Jun 2020 07:53:01: 2000000 INFO @ Fri, 26 Jun 2020 07:53:01: 9000000 INFO @ Fri, 26 Jun 2020 07:53:08: 6000000 INFO @ Fri, 26 Jun 2020 07:53:11: 3000000 INFO @ Fri, 26 Jun 2020 07:53:12: 10000000 INFO @ Fri, 26 Jun 2020 07:53:19: 7000000 INFO @ Fri, 26 Jun 2020 07:53:22: 4000000 INFO @ Fri, 26 Jun 2020 07:53:22: 11000000 INFO @ Fri, 26 Jun 2020 07:53:29: 8000000 INFO @ Fri, 26 Jun 2020 07:53:32: 5000000 INFO @ Fri, 26 Jun 2020 07:53:33: 12000000 INFO @ Fri, 26 Jun 2020 07:53:39: 9000000 INFO @ Fri, 26 Jun 2020 07:53:43: 6000000 INFO @ Fri, 26 Jun 2020 07:53:44: 13000000 INFO @ Fri, 26 Jun 2020 07:53:50: 10000000 INFO @ Fri, 26 Jun 2020 07:53:53: 7000000 INFO @ Fri, 26 Jun 2020 07:53:55: 14000000 INFO @ Fri, 26 Jun 2020 07:54:00: 11000000 INFO @ Fri, 26 Jun 2020 07:54:03: 8000000 INFO @ Fri, 26 Jun 2020 07:54:05: 15000000 INFO @ Fri, 26 Jun 2020 07:54:11: 12000000 INFO @ Fri, 26 Jun 2020 07:54:13: 9000000 INFO @ Fri, 26 Jun 2020 07:54:15: 16000000 INFO @ Fri, 26 Jun 2020 07:54:22: 13000000 INFO @ Fri, 26 Jun 2020 07:54:23: 10000000 INFO @ Fri, 26 Jun 2020 07:54:26: 17000000 INFO @ Fri, 26 Jun 2020 07:54:32: 14000000 INFO @ Fri, 26 Jun 2020 07:54:33: 11000000 INFO @ Fri, 26 Jun 2020 07:54:36: 18000000 INFO @ Fri, 26 Jun 2020 07:54:42: 15000000 INFO @ Fri, 26 Jun 2020 07:54:43: 12000000 INFO @ Fri, 26 Jun 2020 07:54:46: 19000000 INFO @ Fri, 26 Jun 2020 07:54:52: 16000000 INFO @ Fri, 26 Jun 2020 07:54:53: 13000000 INFO @ Fri, 26 Jun 2020 07:54:56: 20000000 INFO @ Fri, 26 Jun 2020 07:55:02: 17000000 INFO @ Fri, 26 Jun 2020 07:55:03: 14000000 INFO @ Fri, 26 Jun 2020 07:55:06: 21000000 INFO @ Fri, 26 Jun 2020 07:55:13: 18000000 INFO @ Fri, 26 Jun 2020 07:55:14: 15000000 INFO @ Fri, 26 Jun 2020 07:55:17: 22000000 INFO @ Fri, 26 Jun 2020 07:55:23: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:55:24: 16000000 INFO @ Fri, 26 Jun 2020 07:55:27: 23000000 INFO @ Fri, 26 Jun 2020 07:55:33: 20000000 INFO @ Fri, 26 Jun 2020 07:55:35: 17000000 INFO @ Fri, 26 Jun 2020 07:55:38: 24000000 INFO @ Fri, 26 Jun 2020 07:55:44: 21000000 INFO @ Fri, 26 Jun 2020 07:55:45: 18000000 INFO @ Fri, 26 Jun 2020 07:55:48: 25000000 INFO @ Fri, 26 Jun 2020 07:55:54: 22000000 INFO @ Fri, 26 Jun 2020 07:55:56: 19000000 INFO @ Fri, 26 Jun 2020 07:55:59: 26000000 INFO @ Fri, 26 Jun 2020 07:56:05: 23000000 INFO @ Fri, 26 Jun 2020 07:56:07: 20000000 INFO @ Fri, 26 Jun 2020 07:56:09: 27000000 INFO @ Fri, 26 Jun 2020 07:56:15: 24000000 INFO @ Fri, 26 Jun 2020 07:56:17: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 07:56:17: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 07:56:17: #1 total tags in treatment: 12378546 INFO @ Fri, 26 Jun 2020 07:56:17: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:56:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:56:17: #1 tags after filtering in treatment: 11203731 INFO @ Fri, 26 Jun 2020 07:56:17: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 07:56:17: #1 finished! INFO @ Fri, 26 Jun 2020 07:56:17: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:56:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:56:18: 21000000 INFO @ Fri, 26 Jun 2020 07:56:18: #2 number of paired peaks: 315 WARNING @ Fri, 26 Jun 2020 07:56:18: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Fri, 26 Jun 2020 07:56:18: start model_add_line... INFO @ Fri, 26 Jun 2020 07:56:18: start X-correlation... INFO @ Fri, 26 Jun 2020 07:56:18: end of X-cor INFO @ Fri, 26 Jun 2020 07:56:18: #2 finished! INFO @ Fri, 26 Jun 2020 07:56:18: #2 predicted fragment length is 164 bps INFO @ Fri, 26 Jun 2020 07:56:18: #2 alternative fragment length(s) may be 164 bps INFO @ Fri, 26 Jun 2020 07:56:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2011721/SRX2011721.05_model.r WARNING @ Fri, 26 Jun 2020 07:56:18: #2 Since the d (164) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:56:18: #2 You may need to consider one of the other alternative d(s): 164 WARNING @ Fri, 26 Jun 2020 07:56:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:56:18: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:56:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:56:25: 25000000 INFO @ Fri, 26 Jun 2020 07:56:28: 22000000 INFO @ Fri, 26 Jun 2020 07:56:36: 26000000 INFO @ Fri, 26 Jun 2020 07:56:39: 23000000 INFO @ Fri, 26 Jun 2020 07:56:44: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:56:46: 27000000 INFO @ Fri, 26 Jun 2020 07:56:50: 24000000 INFO @ Fri, 26 Jun 2020 07:56:53: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 07:56:53: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 07:56:53: #1 total tags in treatment: 12378546 INFO @ Fri, 26 Jun 2020 07:56:53: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:56:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:56:53: #1 tags after filtering in treatment: 11203731 INFO @ Fri, 26 Jun 2020 07:56:53: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 07:56:53: #1 finished! INFO @ Fri, 26 Jun 2020 07:56:53: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:56:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:56:54: #2 number of paired peaks: 315 WARNING @ Fri, 26 Jun 2020 07:56:54: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Fri, 26 Jun 2020 07:56:54: start model_add_line... INFO @ Fri, 26 Jun 2020 07:56:54: start X-correlation... INFO @ Fri, 26 Jun 2020 07:56:54: end of X-cor INFO @ Fri, 26 Jun 2020 07:56:54: #2 finished! INFO @ Fri, 26 Jun 2020 07:56:54: #2 predicted fragment length is 164 bps INFO @ Fri, 26 Jun 2020 07:56:54: #2 alternative fragment length(s) may be 164 bps INFO @ Fri, 26 Jun 2020 07:56:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2011721/SRX2011721.10_model.r WARNING @ Fri, 26 Jun 2020 07:56:54: #2 Since the d (164) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:56:54: #2 You may need to consider one of the other alternative d(s): 164 WARNING @ Fri, 26 Jun 2020 07:56:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:56:54: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:56:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:56:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2011721/SRX2011721.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:56:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2011721/SRX2011721.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:56:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2011721/SRX2011721.05_summits.bed INFO @ Fri, 26 Jun 2020 07:56:56: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (395 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:57:00: 25000000 INFO @ Fri, 26 Jun 2020 07:57:09: 26000000 INFO @ Fri, 26 Jun 2020 07:57:18: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:57:19: 27000000 INFO @ Fri, 26 Jun 2020 07:57:26: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 07:57:26: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 07:57:26: #1 total tags in treatment: 12378546 INFO @ Fri, 26 Jun 2020 07:57:26: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:57:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:57:26: #1 tags after filtering in treatment: 11203731 INFO @ Fri, 26 Jun 2020 07:57:26: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 07:57:26: #1 finished! INFO @ Fri, 26 Jun 2020 07:57:26: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:57:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:57:27: #2 number of paired peaks: 315 WARNING @ Fri, 26 Jun 2020 07:57:27: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Fri, 26 Jun 2020 07:57:27: start model_add_line... INFO @ Fri, 26 Jun 2020 07:57:27: start X-correlation... INFO @ Fri, 26 Jun 2020 07:57:27: end of X-cor INFO @ Fri, 26 Jun 2020 07:57:27: #2 finished! INFO @ Fri, 26 Jun 2020 07:57:27: #2 predicted fragment length is 164 bps INFO @ Fri, 26 Jun 2020 07:57:27: #2 alternative fragment length(s) may be 164 bps INFO @ Fri, 26 Jun 2020 07:57:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2011721/SRX2011721.20_model.r WARNING @ Fri, 26 Jun 2020 07:57:27: #2 Since the d (164) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:57:27: #2 You may need to consider one of the other alternative d(s): 164 WARNING @ Fri, 26 Jun 2020 07:57:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:57:27: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:57:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:57:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2011721/SRX2011721.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:57:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2011721/SRX2011721.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:57:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2011721/SRX2011721.10_summits.bed INFO @ Fri, 26 Jun 2020 07:57:30: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (300 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:57:51: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:58:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2011721/SRX2011721.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:58:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2011721/SRX2011721.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:58:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2011721/SRX2011721.20_summits.bed INFO @ Fri, 26 Jun 2020 07:58:03: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (205 records, 4 fields): 2 millis CompletedMACS2peakCalling