Job ID = 6497391 SRX = SRX4085411 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T21:29:50 prefetch.2.10.7: 1) Downloading 'SRR7167440'... 2020-06-25T21:29:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:35:29 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:35:29 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:29 23049643 reads; of these: 23049643 (100.00%) were paired; of these: 16405341 (71.17%) aligned concordantly 0 times 5502832 (23.87%) aligned concordantly exactly 1 time 1141470 (4.95%) aligned concordantly >1 times ---- 16405341 pairs aligned concordantly 0 times; of these: 273864 (1.67%) aligned discordantly 1 time ---- 16131477 pairs aligned 0 times concordantly or discordantly; of these: 32262954 mates make up the pairs; of these: 26935395 (83.49%) aligned 0 times 4777062 (14.81%) aligned exactly 1 time 550497 (1.71%) aligned >1 times 41.57% overall alignment rate Time searching: 00:11:29 Overall time: 00:11:29 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 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] 759035 / 6812398 = 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 06:56:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085411/SRX4085411.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085411/SRX4085411.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085411/SRX4085411.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 06:56:44: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:56:44: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:56:50: 1000000 INFO @ Fri, 26 Jun 2020 06:56:56: 2000000 INFO @ Fri, 26 Jun 2020 06:57:02: 3000000 INFO @ Fri, 26 Jun 2020 06:57:08: 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 06:57:13: 5000000 INFO @ Fri, 26 Jun 2020 06:57:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085411/SRX4085411.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085411/SRX4085411.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085411/SRX4085411.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 06:57:14: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:57:14: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:57:20: 6000000 INFO @ Fri, 26 Jun 2020 06:57:20: 1000000 INFO @ Fri, 26 Jun 2020 06:57:26: 7000000 INFO @ Fri, 26 Jun 2020 06:57:26: 2000000 INFO @ Fri, 26 Jun 2020 06:57:33: 8000000 INFO @ Fri, 26 Jun 2020 06:57:33: 3000000 INFO @ Fri, 26 Jun 2020 06:57:39: 4000000 INFO @ Fri, 26 Jun 2020 06:57:40: 9000000 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 06:57:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085411/SRX4085411.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085411/SRX4085411.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085411/SRX4085411.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 06:57:44: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:57:44: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:57:46: 5000000 INFO @ Fri, 26 Jun 2020 06:57:48: 10000000 INFO @ Fri, 26 Jun 2020 06:57:51: 1000000 INFO @ Fri, 26 Jun 2020 06:57:52: 6000000 INFO @ Fri, 26 Jun 2020 06:57:56: 11000000 INFO @ Fri, 26 Jun 2020 06:57:58: 2000000 INFO @ Fri, 26 Jun 2020 06:57:59: 7000000 INFO @ Fri, 26 Jun 2020 06:58:02: 12000000 INFO @ Fri, 26 Jun 2020 06:58:05: 3000000 INFO @ Fri, 26 Jun 2020 06:58:06: 8000000 INFO @ Fri, 26 Jun 2020 06:58:10: 13000000 INFO @ Fri, 26 Jun 2020 06:58:11: 4000000 INFO @ Fri, 26 Jun 2020 06:58:12: 9000000 INFO @ Fri, 26 Jun 2020 06:58:18: 14000000 INFO @ Fri, 26 Jun 2020 06:58:18: 5000000 INFO @ Fri, 26 Jun 2020 06:58:18: 10000000 INFO @ Fri, 26 Jun 2020 06:58:24: 6000000 INFO @ Fri, 26 Jun 2020 06:58:25: 11000000 INFO @ Fri, 26 Jun 2020 06:58:26: 15000000 INFO @ Fri, 26 Jun 2020 06:58:31: 7000000 INFO @ Fri, 26 Jun 2020 06:58:31: 12000000 INFO @ Fri, 26 Jun 2020 06:58:33: 16000000 INFO @ Fri, 26 Jun 2020 06:58:37: 8000000 INFO @ Fri, 26 Jun 2020 06:58:38: 13000000 INFO @ Fri, 26 Jun 2020 06:58:39: 17000000 INFO @ Fri, 26 Jun 2020 06:58:43: 9000000 INFO @ Fri, 26 Jun 2020 06:58:43: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 06:58:43: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 06:58:43: #1 total tags in treatment: 5906484 INFO @ Fri, 26 Jun 2020 06:58:43: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:58:43: #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 06:58:43: #1 tags after filtering in treatment: 5012345 INFO @ Fri, 26 Jun 2020 06:58:43: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 26 Jun 2020 06:58:43: #1 finished! INFO @ Fri, 26 Jun 2020 06:58:43: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:58:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:58:44: #2 number of paired peaks: 898 WARNING @ Fri, 26 Jun 2020 06:58:44: Fewer paired peaks (898) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 898 pairs to build model! INFO @ Fri, 26 Jun 2020 06:58:44: start model_add_line... INFO @ Fri, 26 Jun 2020 06:58:44: start X-correlation... INFO @ Fri, 26 Jun 2020 06:58:44: end of X-cor INFO @ Fri, 26 Jun 2020 06:58:44: #2 finished! INFO @ Fri, 26 Jun 2020 06:58:44: #2 predicted fragment length is 88 bps INFO @ Fri, 26 Jun 2020 06:58:44: #2 alternative fragment length(s) may be 88 bps INFO @ Fri, 26 Jun 2020 06:58:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085411/SRX4085411.05_model.r WARNING @ Fri, 26 Jun 2020 06:58:44: #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 06:58:44: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Fri, 26 Jun 2020 06:58:44: #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 06:58:44: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:58:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:58:45: 14000000 INFO @ Fri, 26 Jun 2020 06:58:49: 10000000 INFO @ Fri, 26 Jun 2020 06:58:51: 15000000 INFO @ Fri, 26 Jun 2020 06:58:54: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:58:55: 11000000 INFO @ Fri, 26 Jun 2020 06:58:57: 16000000 INFO @ Fri, 26 Jun 2020 06:59:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085411/SRX4085411.05_peaks.xls INFO @ Fri, 26 Jun 2020 06:59:01: 12000000 INFO @ Fri, 26 Jun 2020 06:59:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085411/SRX4085411.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:59:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085411/SRX4085411.05_summits.bed INFO @ Fri, 26 Jun 2020 06:59:02: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4886 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 06:59:03: 17000000 INFO @ Fri, 26 Jun 2020 06:59:06: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 06:59:06: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 06:59:06: #1 total tags in treatment: 5906484 INFO @ Fri, 26 Jun 2020 06:59:06: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:59:06: #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 06:59:06: #1 tags after filtering in treatment: 5012345 INFO @ Fri, 26 Jun 2020 06:59:06: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 26 Jun 2020 06:59:06: #1 finished! INFO @ Fri, 26 Jun 2020 06:59:06: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:59:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:59:07: #2 number of paired peaks: 898 WARNING @ Fri, 26 Jun 2020 06:59:07: Fewer paired peaks (898) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 898 pairs to build model! INFO @ Fri, 26 Jun 2020 06:59:07: start model_add_line... INFO @ Fri, 26 Jun 2020 06:59:07: start X-correlation... INFO @ Fri, 26 Jun 2020 06:59:07: end of X-cor INFO @ Fri, 26 Jun 2020 06:59:07: #2 finished! INFO @ Fri, 26 Jun 2020 06:59:07: #2 predicted fragment length is 88 bps INFO @ Fri, 26 Jun 2020 06:59:07: #2 alternative fragment length(s) may be 88 bps INFO @ Fri, 26 Jun 2020 06:59:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085411/SRX4085411.10_model.r INFO @ Fri, 26 Jun 2020 06:59:07: 13000000 WARNING @ Fri, 26 Jun 2020 06:59:12: #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 06:59:12: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Fri, 26 Jun 2020 06:59:12: #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 06:59:12: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:59:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:59:13: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 06:59:19: 15000000 INFO @ Fri, 26 Jun 2020 06:59:22: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:59:25: 16000000 INFO @ Fri, 26 Jun 2020 06:59:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085411/SRX4085411.10_peaks.xls INFO @ Fri, 26 Jun 2020 06:59:30: 17000000 INFO @ Fri, 26 Jun 2020 06:59:33: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 06:59:33: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 06:59:33: #1 total tags in treatment: 5906484 INFO @ Fri, 26 Jun 2020 06:59:33: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:59:33: #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 06:59:33: #1 tags after filtering in treatment: 5012345 INFO @ Fri, 26 Jun 2020 06:59:33: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 26 Jun 2020 06:59:33: #1 finished! INFO @ Fri, 26 Jun 2020 06:59:33: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:59:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:59:34: #2 number of paired peaks: 898 WARNING @ Fri, 26 Jun 2020 06:59:34: Fewer paired peaks (898) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 898 pairs to build model! INFO @ Fri, 26 Jun 2020 06:59:34: start model_add_line... INFO @ Fri, 26 Jun 2020 06:59:34: start X-correlation... INFO @ Fri, 26 Jun 2020 06:59:34: end of X-cor INFO @ Fri, 26 Jun 2020 06:59:34: #2 finished! INFO @ Fri, 26 Jun 2020 06:59:34: #2 predicted fragment length is 88 bps INFO @ Fri, 26 Jun 2020 06:59:34: #2 alternative fragment length(s) may be 88 bps INFO @ Fri, 26 Jun 2020 06:59:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085411/SRX4085411.20_model.r WARNING @ Fri, 26 Jun 2020 06:59:34: #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 06:59:34: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Fri, 26 Jun 2020 06:59:34: #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 06:59:34: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:59:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:59:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085411/SRX4085411.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:59:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085411/SRX4085411.10_summits.bed INFO @ Fri, 26 Jun 2020 06:59:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2888 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 06:59:44: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:59:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085411/SRX4085411.20_peaks.xls INFO @ Fri, 26 Jun 2020 06:59:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085411/SRX4085411.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:59:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085411/SRX4085411.20_summits.bed INFO @ Fri, 26 Jun 2020 06:59:49: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1431 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。