Job ID = 8069360 SRX = SRX7217778 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:31:22 prefetch.2.10.7: 1) Downloading 'SRR10533855'... 2020-08-08T03:31:22 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:33:08 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:33:08 prefetch.2.10.7: 1) 'SRR10533855' was downloaded successfully 2020-08-08T03:33:08 prefetch.2.10.7: 'SRR10533855' has 0 unresolved dependencies Read 7928426 spots for SRR10533855/SRR10533855.sra Written 7928426 spots for SRR10533855/SRR10533855.sra fastq に変換しました。 bowtie でマッピング中... Your job 8070297 ("srTce11") 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: 00:14:05 7928426 reads; of these: 7928426 (100.00%) were paired; of these: 1780481 (22.46%) aligned concordantly 0 times 5308755 (66.96%) aligned concordantly exactly 1 time 839190 (10.58%) aligned concordantly >1 times ---- 1780481 pairs aligned concordantly 0 times; of these: 572177 (32.14%) aligned discordantly 1 time ---- 1208304 pairs aligned 0 times concordantly or discordantly; of these: 2416608 mates make up the pairs; of these: 2173213 (89.93%) aligned 0 times 133674 (5.53%) aligned exactly 1 time 109721 (4.54%) aligned >1 times 86.29% overall alignment rate Time searching: 00:14:05 Overall time: 00:14:05 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 12 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] 969040 / 6680710 = 0.1451 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 @ Sat, 08 Aug 2020 12:53:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217778/SRX7217778.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217778/SRX7217778.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217778/SRX7217778.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217778/SRX7217778.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 @ Sat, 08 Aug 2020 12:53:48: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:53:48: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:53:58: 1000000 INFO @ Sat, 08 Aug 2020 12:54:08: 2000000 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 @ Sat, 08 Aug 2020 12:54:18: 3000000 INFO @ Sat, 08 Aug 2020 12:54:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217778/SRX7217778.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217778/SRX7217778.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217778/SRX7217778.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217778/SRX7217778.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 @ Sat, 08 Aug 2020 12:54:18: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:54:18: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:54:29: 1000000 INFO @ Sat, 08 Aug 2020 12:54:29: 4000000 INFO @ Sat, 08 Aug 2020 12:54:39: 2000000 INFO @ Sat, 08 Aug 2020 12:54:41: 5000000 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 @ Sat, 08 Aug 2020 12:54:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217778/SRX7217778.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217778/SRX7217778.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217778/SRX7217778.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217778/SRX7217778.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 @ Sat, 08 Aug 2020 12:54:48: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:54:48: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:54:49: 3000000 INFO @ Sat, 08 Aug 2020 12:54:52: 6000000 INFO @ Sat, 08 Aug 2020 12:54:59: 1000000 INFO @ Sat, 08 Aug 2020 12:55:00: 4000000 INFO @ Sat, 08 Aug 2020 12:55:04: 7000000 INFO @ Sat, 08 Aug 2020 12:55:10: 2000000 INFO @ Sat, 08 Aug 2020 12:55:10: 5000000 INFO @ Sat, 08 Aug 2020 12:55:16: 8000000 INFO @ Sat, 08 Aug 2020 12:55:20: 3000000 INFO @ Sat, 08 Aug 2020 12:55:20: 6000000 INFO @ Sat, 08 Aug 2020 12:55:28: 9000000 INFO @ Sat, 08 Aug 2020 12:55:30: 4000000 INFO @ Sat, 08 Aug 2020 12:55:30: 7000000 INFO @ Sat, 08 Aug 2020 12:55:40: 10000000 INFO @ Sat, 08 Aug 2020 12:55:40: 5000000 INFO @ Sat, 08 Aug 2020 12:55:40: 8000000 INFO @ Sat, 08 Aug 2020 12:55:51: 9000000 INFO @ Sat, 08 Aug 2020 12:55:51: 6000000 INFO @ Sat, 08 Aug 2020 12:55:52: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 12:56:00: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:56:00: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:56:00: #1 total tags in treatment: 5245502 INFO @ Sat, 08 Aug 2020 12:56:00: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:56:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:56:00: #1 tags after filtering in treatment: 4837034 INFO @ Sat, 08 Aug 2020 12:56:00: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 12:56:00: #1 finished! INFO @ Sat, 08 Aug 2020 12:56:00: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:56:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:56:01: 10000000 INFO @ Sat, 08 Aug 2020 12:56:01: #2 number of paired peaks: 421 WARNING @ Sat, 08 Aug 2020 12:56:01: Fewer paired peaks (421) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 421 pairs to build model! INFO @ Sat, 08 Aug 2020 12:56:01: start model_add_line... INFO @ Sat, 08 Aug 2020 12:56:01: 7000000 INFO @ Sat, 08 Aug 2020 12:56:01: start X-correlation... INFO @ Sat, 08 Aug 2020 12:56:01: end of X-cor INFO @ Sat, 08 Aug 2020 12:56:01: #2 finished! INFO @ Sat, 08 Aug 2020 12:56:01: #2 predicted fragment length is 209 bps INFO @ Sat, 08 Aug 2020 12:56:01: #2 alternative fragment length(s) may be 209 bps INFO @ Sat, 08 Aug 2020 12:56:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217778/SRX7217778.05_model.r WARNING @ Sat, 08 Aug 2020 12:56:01: #2 Since the d (209) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:56:01: #2 You may need to consider one of the other alternative d(s): 209 WARNING @ Sat, 08 Aug 2020 12:56:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 12:56:01: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:56:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:56:10: 11000000 INFO @ Sat, 08 Aug 2020 12:56:10: 8000000 INFO @ Sat, 08 Aug 2020 12:56:11: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:56:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217778/SRX7217778.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:56:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217778/SRX7217778.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:56:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217778/SRX7217778.05_summits.bed INFO @ Sat, 08 Aug 2020 12:56:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (307 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:56:17: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:56:17: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:56:17: #1 total tags in treatment: 5245502 INFO @ Sat, 08 Aug 2020 12:56:17: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:56:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:56:17: #1 tags after filtering in treatment: 4837034 INFO @ Sat, 08 Aug 2020 12:56:17: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 12:56:17: #1 finished! INFO @ Sat, 08 Aug 2020 12:56:17: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:56:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:56:18: #2 number of paired peaks: 421 WARNING @ Sat, 08 Aug 2020 12:56:18: Fewer paired peaks (421) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 421 pairs to build model! INFO @ Sat, 08 Aug 2020 12:56:18: start model_add_line... INFO @ Sat, 08 Aug 2020 12:56:18: start X-correlation... INFO @ Sat, 08 Aug 2020 12:56:18: end of X-cor INFO @ Sat, 08 Aug 2020 12:56:18: #2 finished! INFO @ Sat, 08 Aug 2020 12:56:18: #2 predicted fragment length is 209 bps INFO @ Sat, 08 Aug 2020 12:56:18: #2 alternative fragment length(s) may be 209 bps INFO @ Sat, 08 Aug 2020 12:56:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217778/SRX7217778.10_model.r WARNING @ Sat, 08 Aug 2020 12:56:18: #2 Since the d (209) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:56:18: #2 You may need to consider one of the other alternative d(s): 209 WARNING @ Sat, 08 Aug 2020 12:56:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 12:56:18: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:56:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:56:20: 9000000 INFO @ Sat, 08 Aug 2020 12:56:28: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:56:29: 10000000 INFO @ Sat, 08 Aug 2020 12:56:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217778/SRX7217778.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:56:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217778/SRX7217778.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:56:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217778/SRX7217778.10_summits.bed INFO @ Sat, 08 Aug 2020 12:56:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (228 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:56:38: 11000000 INFO @ Sat, 08 Aug 2020 12:56:44: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:56:44: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:56:44: #1 total tags in treatment: 5245502 INFO @ Sat, 08 Aug 2020 12:56:44: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:56:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:56:44: #1 tags after filtering in treatment: 4837034 INFO @ Sat, 08 Aug 2020 12:56:44: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 12:56:44: #1 finished! INFO @ Sat, 08 Aug 2020 12:56:44: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:56:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:56:44: #2 number of paired peaks: 421 WARNING @ Sat, 08 Aug 2020 12:56:44: Fewer paired peaks (421) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 421 pairs to build model! INFO @ Sat, 08 Aug 2020 12:56:44: start model_add_line... INFO @ Sat, 08 Aug 2020 12:56:44: start X-correlation... INFO @ Sat, 08 Aug 2020 12:56:44: end of X-cor INFO @ Sat, 08 Aug 2020 12:56:44: #2 finished! INFO @ Sat, 08 Aug 2020 12:56:44: #2 predicted fragment length is 209 bps INFO @ Sat, 08 Aug 2020 12:56:44: #2 alternative fragment length(s) may be 209 bps INFO @ Sat, 08 Aug 2020 12:56:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217778/SRX7217778.20_model.r WARNING @ Sat, 08 Aug 2020 12:56:45: #2 Since the d (209) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:56:45: #2 You may need to consider one of the other alternative d(s): 209 WARNING @ Sat, 08 Aug 2020 12:56:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 12:56:45: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:56:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:56:55: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:57:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217778/SRX7217778.20_peaks.xls INFO @ Sat, 08 Aug 2020 12:57:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217778/SRX7217778.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:57:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217778/SRX7217778.20_summits.bed INFO @ Sat, 08 Aug 2020 12:57:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (169 records, 4 fields): 8 millis CompletedMACS2peakCalling