Job ID = 6367811 SRX = SRX4085379 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:40:59 prefetch.2.10.7: 1) Downloading 'SRR7167408'... 2020-06-15T23:40:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:46:34 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:46:34 prefetch.2.10.7: 1) 'SRR7167408' was downloaded successfully Read 15617541 spots for SRR7167408/SRR7167408.sra Written 15617541 spots for SRR7167408/SRR7167408.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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:16 15617541 reads; of these: 15617541 (100.00%) were paired; of these: 10034259 (64.25%) aligned concordantly 0 times 4859954 (31.12%) aligned concordantly exactly 1 time 723328 (4.63%) aligned concordantly >1 times ---- 10034259 pairs aligned concordantly 0 times; of these: 385642 (3.84%) aligned discordantly 1 time ---- 9648617 pairs aligned 0 times concordantly or discordantly; of these: 19297234 mates make up the pairs; of these: 13449283 (69.70%) aligned 0 times 5182418 (26.86%) aligned exactly 1 time 665533 (3.45%) aligned >1 times 56.94% overall alignment rate Time searching: 00:08:16 Overall time: 00:08:16 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 8 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] 329644 / 5820400 = 0.0566 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 @ Tue, 16 Jun 2020 09:01:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085379/SRX4085379.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085379/SRX4085379.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085379/SRX4085379.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085379/SRX4085379.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 @ Tue, 16 Jun 2020 09:01:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:01:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:01:35: 1000000 INFO @ Tue, 16 Jun 2020 09:01:40: 2000000 INFO @ Tue, 16 Jun 2020 09:01:44: 3000000 INFO @ Tue, 16 Jun 2020 09:01:49: 4000000 INFO @ Tue, 16 Jun 2020 09:01:54: 5000000 INFO @ Tue, 16 Jun 2020 09:01:58: 6000000 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 @ Tue, 16 Jun 2020 09:02:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085379/SRX4085379.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085379/SRX4085379.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085379/SRX4085379.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085379/SRX4085379.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 @ Tue, 16 Jun 2020 09:02:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:02:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:02:03: 7000000 INFO @ Tue, 16 Jun 2020 09:02:06: 1000000 INFO @ Tue, 16 Jun 2020 09:02:08: 8000000 INFO @ Tue, 16 Jun 2020 09:02:12: 2000000 INFO @ Tue, 16 Jun 2020 09:02:14: 9000000 INFO @ Tue, 16 Jun 2020 09:02:17: 3000000 INFO @ Tue, 16 Jun 2020 09:02:19: 10000000 INFO @ Tue, 16 Jun 2020 09:02:23: 4000000 INFO @ Tue, 16 Jun 2020 09:02:24: 11000000 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 @ Tue, 16 Jun 2020 09:02:29: 5000000 INFO @ Tue, 16 Jun 2020 09:02:29: 12000000 INFO @ Tue, 16 Jun 2020 09:02:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085379/SRX4085379.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085379/SRX4085379.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085379/SRX4085379.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085379/SRX4085379.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 @ Tue, 16 Jun 2020 09:02:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:02:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:02:34: 13000000 INFO @ Tue, 16 Jun 2020 09:02:35: 6000000 INFO @ Tue, 16 Jun 2020 09:02:36: 1000000 INFO @ Tue, 16 Jun 2020 09:02:39: 14000000 INFO @ Tue, 16 Jun 2020 09:02:41: 7000000 INFO @ Tue, 16 Jun 2020 09:02:41: 2000000 INFO @ Tue, 16 Jun 2020 09:02:45: 15000000 INFO @ Tue, 16 Jun 2020 09:02:46: 3000000 INFO @ Tue, 16 Jun 2020 09:02:47: 8000000 INFO @ Tue, 16 Jun 2020 09:02:50: 16000000 INFO @ Tue, 16 Jun 2020 09:02:51: 4000000 INFO @ Tue, 16 Jun 2020 09:02:53: 9000000 INFO @ Tue, 16 Jun 2020 09:02:55: 17000000 INFO @ Tue, 16 Jun 2020 09:02:56: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:02:56: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:02:56: #1 total tags in treatment: 5266530 INFO @ Tue, 16 Jun 2020 09:02:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:02:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:02:56: #1 tags after filtering in treatment: 4824740 INFO @ Tue, 16 Jun 2020 09:02:56: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 09:02:56: #1 finished! INFO @ Tue, 16 Jun 2020 09:02:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:02:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:02:56: #2 number of paired peaks: 339 WARNING @ Tue, 16 Jun 2020 09:02:56: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Tue, 16 Jun 2020 09:02:56: start model_add_line... INFO @ Tue, 16 Jun 2020 09:02:56: start X-correlation... INFO @ Tue, 16 Jun 2020 09:02:56: end of X-cor INFO @ Tue, 16 Jun 2020 09:02:56: #2 finished! INFO @ Tue, 16 Jun 2020 09:02:56: #2 predicted fragment length is 72 bps INFO @ Tue, 16 Jun 2020 09:02:56: #2 alternative fragment length(s) may be 72 bps INFO @ Tue, 16 Jun 2020 09:02:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085379/SRX4085379.05_model.r WARNING @ Tue, 16 Jun 2020 09:02:56: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:02:56: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Tue, 16 Jun 2020 09:02:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:02:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:02:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:02:57: 5000000 INFO @ Tue, 16 Jun 2020 09:02:58: 10000000 INFO @ Tue, 16 Jun 2020 09:03:02: 6000000 INFO @ Tue, 16 Jun 2020 09:03:05: 11000000 INFO @ Tue, 16 Jun 2020 09:03:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:03:07: 7000000 INFO @ Tue, 16 Jun 2020 09:03:11: 12000000 INFO @ Tue, 16 Jun 2020 09:03:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085379/SRX4085379.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:03:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085379/SRX4085379.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:03:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085379/SRX4085379.05_summits.bed INFO @ Tue, 16 Jun 2020 09:03:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1474 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:03:12: 8000000 INFO @ Tue, 16 Jun 2020 09:03:17: 13000000 INFO @ Tue, 16 Jun 2020 09:03:17: 9000000 INFO @ Tue, 16 Jun 2020 09:03:23: 10000000 INFO @ Tue, 16 Jun 2020 09:03:23: 14000000 INFO @ Tue, 16 Jun 2020 09:03:28: 11000000 INFO @ Tue, 16 Jun 2020 09:03:29: 15000000 INFO @ Tue, 16 Jun 2020 09:03:33: 12000000 INFO @ Tue, 16 Jun 2020 09:03:35: 16000000 INFO @ Tue, 16 Jun 2020 09:03:39: 13000000 INFO @ Tue, 16 Jun 2020 09:03:41: 17000000 INFO @ Tue, 16 Jun 2020 09:03:42: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:03:42: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:03:42: #1 total tags in treatment: 5266530 INFO @ Tue, 16 Jun 2020 09:03:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:03:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:03:42: #1 tags after filtering in treatment: 4824740 INFO @ Tue, 16 Jun 2020 09:03:42: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 09:03:42: #1 finished! INFO @ Tue, 16 Jun 2020 09:03:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:03:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:03:42: #2 number of paired peaks: 339 WARNING @ Tue, 16 Jun 2020 09:03:42: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Tue, 16 Jun 2020 09:03:42: start model_add_line... INFO @ Tue, 16 Jun 2020 09:03:42: start X-correlation... INFO @ Tue, 16 Jun 2020 09:03:42: end of X-cor INFO @ Tue, 16 Jun 2020 09:03:42: #2 finished! INFO @ Tue, 16 Jun 2020 09:03:42: #2 predicted fragment length is 72 bps INFO @ Tue, 16 Jun 2020 09:03:42: #2 alternative fragment length(s) may be 72 bps INFO @ Tue, 16 Jun 2020 09:03:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085379/SRX4085379.10_model.r WARNING @ Tue, 16 Jun 2020 09:03:42: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:03:42: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Tue, 16 Jun 2020 09:03:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:03:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:03:42: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:03:44: 14000000 INFO @ Tue, 16 Jun 2020 09:03:49: 15000000 INFO @ Tue, 16 Jun 2020 09:03:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:03:54: 16000000 INFO @ Tue, 16 Jun 2020 09:03:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085379/SRX4085379.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:03:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085379/SRX4085379.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:03:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085379/SRX4085379.10_summits.bed INFO @ Tue, 16 Jun 2020 09:03:58: Done! INFO @ Tue, 16 Jun 2020 09:03:58: 17000000 INFO @ Tue, 16 Jun 2020 09:03:59: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:03:59: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:03:59: #1 total tags in treatment: 5266530 INFO @ Tue, 16 Jun 2020 09:03:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:03:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:03:59: #1 tags after filtering in treatment: 4824740 INFO @ Tue, 16 Jun 2020 09:03:59: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 09:03:59: #1 finished! INFO @ Tue, 16 Jun 2020 09:03:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:03:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:03:59: #2 number of paired peaks: 339 WARNING @ Tue, 16 Jun 2020 09:03:59: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Tue, 16 Jun 2020 09:03:59: start model_add_line... INFO @ Tue, 16 Jun 2020 09:03:59: start X-correlation... INFO @ Tue, 16 Jun 2020 09:03:59: end of X-cor INFO @ Tue, 16 Jun 2020 09:03:59: #2 finished! INFO @ Tue, 16 Jun 2020 09:03:59: #2 predicted fragment length is 72 bps INFO @ Tue, 16 Jun 2020 09:03:59: #2 alternative fragment length(s) may be 72 bps INFO @ Tue, 16 Jun 2020 09:03:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085379/SRX4085379.20_model.r WARNING @ Tue, 16 Jun 2020 09:03:59: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:03:59: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Tue, 16 Jun 2020 09:03:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:03:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:03:59: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (575 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:04:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:04:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085379/SRX4085379.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:04:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085379/SRX4085379.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:04:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085379/SRX4085379.20_summits.bed INFO @ Tue, 16 Jun 2020 09:04:15: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (118 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。