Job ID = 6507794 SRX = SRX4085411 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T13:12:34 prefetch.2.10.7: 1) Downloading 'SRR7167440'... 2020-06-26T13:12:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:16:15 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:16:15 prefetch.2.10.7: 1) 'SRR7167440' was downloaded successfully Read 23049643 spots for SRR7167440/SRR7167440.sra Written 23049643 spots for SRR7167440/SRR7167440.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: 00:11:33 23049643 reads; of these: 23049643 (100.00%) were paired; of these: 16405073 (71.17%) aligned concordantly 0 times 5503043 (23.87%) aligned concordantly exactly 1 time 1141527 (4.95%) aligned concordantly >1 times ---- 16405073 pairs aligned concordantly 0 times; of these: 273909 (1.67%) aligned discordantly 1 time ---- 16131164 pairs aligned 0 times concordantly or discordantly; of these: 32262328 mates make up the pairs; of these: 26934276 (83.49%) aligned 0 times 4777534 (14.81%) aligned exactly 1 time 550518 (1.71%) aligned >1 times 41.57% overall alignment rate Time searching: 00:11:34 Overall time: 00:11:34 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] 759067 / 6812703 = 0.1114 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 22:36:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085411/SRX4085411.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085411/SRX4085411.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085411/SRX4085411.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085411/SRX4085411.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 22:36:15: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:36:15: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:36:22: 1000000 INFO @ Fri, 26 Jun 2020 22:36:29: 2000000 INFO @ Fri, 26 Jun 2020 22:36:36: 3000000 INFO @ Fri, 26 Jun 2020 22:36:43: 4000000 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 22:36:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085411/SRX4085411.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085411/SRX4085411.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085411/SRX4085411.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085411/SRX4085411.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 22:36:45: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:36:45: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:36:50: 5000000 INFO @ Fri, 26 Jun 2020 22:36:52: 1000000 INFO @ Fri, 26 Jun 2020 22:36:58: 6000000 INFO @ Fri, 26 Jun 2020 22:37:00: 2000000 INFO @ Fri, 26 Jun 2020 22:37:05: 7000000 INFO @ Fri, 26 Jun 2020 22:37:08: 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 22:37:13: 8000000 INFO @ Fri, 26 Jun 2020 22:37:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085411/SRX4085411.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085411/SRX4085411.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085411/SRX4085411.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085411/SRX4085411.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 22:37:15: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:37:15: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:37:15: 4000000 INFO @ Fri, 26 Jun 2020 22:37:21: 9000000 INFO @ Fri, 26 Jun 2020 22:37:23: 1000000 INFO @ Fri, 26 Jun 2020 22:37:23: 5000000 INFO @ Fri, 26 Jun 2020 22:37:29: 10000000 INFO @ Fri, 26 Jun 2020 22:37:30: 2000000 INFO @ Fri, 26 Jun 2020 22:37:31: 6000000 INFO @ Fri, 26 Jun 2020 22:37:37: 11000000 INFO @ Fri, 26 Jun 2020 22:37:38: 3000000 INFO @ Fri, 26 Jun 2020 22:37:38: 7000000 INFO @ Fri, 26 Jun 2020 22:37:44: 12000000 INFO @ Fri, 26 Jun 2020 22:37:46: 4000000 INFO @ Fri, 26 Jun 2020 22:37:46: 8000000 INFO @ Fri, 26 Jun 2020 22:37:52: 13000000 INFO @ Fri, 26 Jun 2020 22:37:54: 5000000 INFO @ Fri, 26 Jun 2020 22:37:54: 9000000 INFO @ Fri, 26 Jun 2020 22:38:00: 14000000 INFO @ Fri, 26 Jun 2020 22:38:02: 6000000 INFO @ Fri, 26 Jun 2020 22:38:02: 10000000 INFO @ Fri, 26 Jun 2020 22:38:08: 15000000 INFO @ Fri, 26 Jun 2020 22:38:10: 7000000 INFO @ Fri, 26 Jun 2020 22:38:10: 11000000 INFO @ Fri, 26 Jun 2020 22:38:16: 16000000 INFO @ Fri, 26 Jun 2020 22:38:18: 8000000 INFO @ Fri, 26 Jun 2020 22:38:19: 12000000 INFO @ Fri, 26 Jun 2020 22:38:24: 17000000 INFO @ Fri, 26 Jun 2020 22:38:26: 9000000 INFO @ Fri, 26 Jun 2020 22:38:27: 13000000 INFO @ Fri, 26 Jun 2020 22:38:29: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 22:38:29: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 22:38:29: #1 total tags in treatment: 5906724 INFO @ Fri, 26 Jun 2020 22:38:29: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:38:29: #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 22:38:29: #1 tags after filtering in treatment: 5012555 INFO @ Fri, 26 Jun 2020 22:38:29: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 26 Jun 2020 22:38:29: #1 finished! INFO @ Fri, 26 Jun 2020 22:38:29: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:38:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:38:29: #2 number of paired peaks: 899 WARNING @ Fri, 26 Jun 2020 22:38:29: Fewer paired peaks (899) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 899 pairs to build model! INFO @ Fri, 26 Jun 2020 22:38:29: start model_add_line... INFO @ Fri, 26 Jun 2020 22:38:29: start X-correlation... INFO @ Fri, 26 Jun 2020 22:38:29: end of X-cor INFO @ Fri, 26 Jun 2020 22:38:29: #2 finished! INFO @ Fri, 26 Jun 2020 22:38:29: #2 predicted fragment length is 88 bps INFO @ Fri, 26 Jun 2020 22:38:29: #2 alternative fragment length(s) may be 88 bps INFO @ Fri, 26 Jun 2020 22:38:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085411/SRX4085411.05_model.r WARNING @ Fri, 26 Jun 2020 22:38:29: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:38:29: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Fri, 26 Jun 2020 22:38:29: #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 22:38:29: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:38:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:38:33: 10000000 INFO @ Fri, 26 Jun 2020 22:38:34: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:38:40: 11000000 INFO @ Fri, 26 Jun 2020 22:38:41: 15000000 INFO @ Fri, 26 Jun 2020 22:38:42: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:38:47: 12000000 INFO @ Fri, 26 Jun 2020 22:38:48: 16000000 INFO @ Fri, 26 Jun 2020 22:38:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085411/SRX4085411.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:38:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085411/SRX4085411.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:38:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085411/SRX4085411.05_summits.bed INFO @ Fri, 26 Jun 2020 22:38:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4881 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:38:54: 17000000 INFO @ Fri, 26 Jun 2020 22:38:54: 13000000 INFO @ Fri, 26 Jun 2020 22:38:58: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 22:38:58: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 22:38:58: #1 total tags in treatment: 5906724 INFO @ Fri, 26 Jun 2020 22:38:58: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:38:58: #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 22:38:58: #1 tags after filtering in treatment: 5012555 INFO @ Fri, 26 Jun 2020 22:38:58: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 26 Jun 2020 22:38:58: #1 finished! INFO @ Fri, 26 Jun 2020 22:38:58: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:38:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:38:59: #2 number of paired peaks: 899 WARNING @ Fri, 26 Jun 2020 22:38:59: Fewer paired peaks (899) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 899 pairs to build model! INFO @ Fri, 26 Jun 2020 22:38:59: start model_add_line... INFO @ Fri, 26 Jun 2020 22:38:59: start X-correlation... INFO @ Fri, 26 Jun 2020 22:38:59: end of X-cor INFO @ Fri, 26 Jun 2020 22:38:59: #2 finished! INFO @ Fri, 26 Jun 2020 22:38:59: #2 predicted fragment length is 88 bps INFO @ Fri, 26 Jun 2020 22:38:59: #2 alternative fragment length(s) may be 88 bps INFO @ Fri, 26 Jun 2020 22:38:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085411/SRX4085411.10_model.r WARNING @ Fri, 26 Jun 2020 22:38:59: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:38:59: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Fri, 26 Jun 2020 22:38:59: #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 22:38:59: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:38:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:39:01: 14000000 INFO @ Fri, 26 Jun 2020 22:39:07: 15000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:39:11: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:39:14: 16000000 INFO @ Fri, 26 Jun 2020 22:39:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085411/SRX4085411.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:39:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085411/SRX4085411.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:39:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085411/SRX4085411.10_summits.bed INFO @ Fri, 26 Jun 2020 22:39:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2889 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:39:19: 17000000 INFO @ Fri, 26 Jun 2020 22:39:23: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 22:39:23: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 22:39:23: #1 total tags in treatment: 5906724 INFO @ Fri, 26 Jun 2020 22:39:23: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:39:23: #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 22:39:23: #1 tags after filtering in treatment: 5012555 INFO @ Fri, 26 Jun 2020 22:39:23: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 26 Jun 2020 22:39:23: #1 finished! INFO @ Fri, 26 Jun 2020 22:39:23: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:39:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:39:24: #2 number of paired peaks: 899 WARNING @ Fri, 26 Jun 2020 22:39:24: Fewer paired peaks (899) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 899 pairs to build model! INFO @ Fri, 26 Jun 2020 22:39:24: start model_add_line... INFO @ Fri, 26 Jun 2020 22:39:24: start X-correlation... INFO @ Fri, 26 Jun 2020 22:39:24: end of X-cor INFO @ Fri, 26 Jun 2020 22:39:24: #2 finished! INFO @ Fri, 26 Jun 2020 22:39:24: #2 predicted fragment length is 88 bps INFO @ Fri, 26 Jun 2020 22:39:24: #2 alternative fragment length(s) may be 88 bps INFO @ Fri, 26 Jun 2020 22:39:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085411/SRX4085411.20_model.r WARNING @ Fri, 26 Jun 2020 22:39:24: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:39:24: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Fri, 26 Jun 2020 22:39:24: #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 22:39:24: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:39:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:39:36: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:39:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085411/SRX4085411.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:39:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085411/SRX4085411.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:39:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085411/SRX4085411.20_summits.bed INFO @ Fri, 26 Jun 2020 22:39:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1431 records, 4 fields): 3 millis CompletedMACS2peakCalling