Job ID = 8069435 SRX = SRX8392421 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:32:44 prefetch.2.10.7: 1) Downloading 'SRR11842074'... 2020-08-08T03:32:44 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:35:37 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:35:37 prefetch.2.10.7: 1) 'SRR11842074' was downloaded successfully 2020-08-08T03:35:37 prefetch.2.10.7: 'SRR11842074' has 0 unresolved dependencies Read 9449036 spots for SRR11842074/SRR11842074.sra Written 9449036 spots for SRR11842074/SRR11842074.sra fastq に変換しました。 bowtie でマッピング中... Your job 8070464 ("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: 00:14:47 9449036 reads; of these: 9449036 (100.00%) were paired; of these: 3638281 (38.50%) aligned concordantly 0 times 4910164 (51.96%) aligned concordantly exactly 1 time 900591 (9.53%) aligned concordantly >1 times ---- 3638281 pairs aligned concordantly 0 times; of these: 1200446 (32.99%) aligned discordantly 1 time ---- 2437835 pairs aligned 0 times concordantly or discordantly; of these: 4875670 mates make up the pairs; of these: 4470903 (91.70%) aligned 0 times 174366 (3.58%) aligned exactly 1 time 230401 (4.73%) aligned >1 times 76.34% overall alignment rate Time searching: 00:14:47 Overall time: 00:14:47 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] 1512077 / 6942507 = 0.2178 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 12:57:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392421/SRX8392421.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392421/SRX8392421.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392421/SRX8392421.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392421/SRX8392421.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 12:57:20: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:57:20: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:57:26: 1000000 INFO @ Sat, 08 Aug 2020 12:57:33: 2000000 INFO @ Sat, 08 Aug 2020 12:57:40: 3000000 INFO @ Sat, 08 Aug 2020 12:57:46: 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 @ Sat, 08 Aug 2020 12:57:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392421/SRX8392421.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392421/SRX8392421.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392421/SRX8392421.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392421/SRX8392421.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 12:57:50: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:57:50: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:57:53: 5000000 INFO @ Sat, 08 Aug 2020 12:57:57: 1000000 INFO @ Sat, 08 Aug 2020 12:58:01: 6000000 INFO @ Sat, 08 Aug 2020 12:58:05: 2000000 INFO @ Sat, 08 Aug 2020 12:58:08: 7000000 INFO @ Sat, 08 Aug 2020 12:58:12: 3000000 INFO @ Sat, 08 Aug 2020 12:58:15: 8000000 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 12:58:19: 4000000 INFO @ Sat, 08 Aug 2020 12:58:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392421/SRX8392421.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392421/SRX8392421.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392421/SRX8392421.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392421/SRX8392421.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 12:58:20: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:58:20: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:58:22: 9000000 INFO @ Sat, 08 Aug 2020 12:58:27: 5000000 INFO @ Sat, 08 Aug 2020 12:58:29: 1000000 INFO @ Sat, 08 Aug 2020 12:58:30: 10000000 INFO @ Sat, 08 Aug 2020 12:58:34: 6000000 INFO @ Sat, 08 Aug 2020 12:58:37: 11000000 INFO @ Sat, 08 Aug 2020 12:58:38: 2000000 INFO @ Sat, 08 Aug 2020 12:58:40: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:58:40: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:58:40: #1 total tags in treatment: 4512306 INFO @ Sat, 08 Aug 2020 12:58:40: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:58:40: #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 12:58:40: #1 tags after filtering in treatment: 4147107 INFO @ Sat, 08 Aug 2020 12:58:40: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 12:58:40: #1 finished! INFO @ Sat, 08 Aug 2020 12:58:40: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:58:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:58:40: #2 number of paired peaks: 520 WARNING @ Sat, 08 Aug 2020 12:58:40: Fewer paired peaks (520) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 520 pairs to build model! INFO @ Sat, 08 Aug 2020 12:58:40: start model_add_line... INFO @ Sat, 08 Aug 2020 12:58:40: start X-correlation... INFO @ Sat, 08 Aug 2020 12:58:40: end of X-cor INFO @ Sat, 08 Aug 2020 12:58:40: #2 finished! INFO @ Sat, 08 Aug 2020 12:58:40: #2 predicted fragment length is 204 bps INFO @ Sat, 08 Aug 2020 12:58:40: #2 alternative fragment length(s) may be 204 bps INFO @ Sat, 08 Aug 2020 12:58:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392421/SRX8392421.05_model.r WARNING @ Sat, 08 Aug 2020 12:58:40: #2 Since the d (204) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:58:40: #2 You may need to consider one of the other alternative d(s): 204 WARNING @ Sat, 08 Aug 2020 12:58:40: #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 12:58:40: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:58:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:58:41: 7000000 INFO @ Sat, 08 Aug 2020 12:58:47: 3000000 INFO @ Sat, 08 Aug 2020 12:58:49: 8000000 INFO @ Sat, 08 Aug 2020 12:58:50: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:58:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392421/SRX8392421.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:58:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392421/SRX8392421.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:58:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392421/SRX8392421.05_summits.bed INFO @ Sat, 08 Aug 2020 12:58:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (654 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:58:56: 9000000 INFO @ Sat, 08 Aug 2020 12:58:56: 4000000 INFO @ Sat, 08 Aug 2020 12:59:03: 10000000 INFO @ Sat, 08 Aug 2020 12:59:05: 5000000 INFO @ Sat, 08 Aug 2020 12:59:11: 11000000 INFO @ Sat, 08 Aug 2020 12:59:14: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:59:14: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:59:14: #1 total tags in treatment: 4512306 INFO @ Sat, 08 Aug 2020 12:59:14: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:59:14: #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 12:59:14: #1 tags after filtering in treatment: 4147107 INFO @ Sat, 08 Aug 2020 12:59:14: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 12:59:14: #1 finished! INFO @ Sat, 08 Aug 2020 12:59:14: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:59:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:59:14: #2 number of paired peaks: 520 WARNING @ Sat, 08 Aug 2020 12:59:14: Fewer paired peaks (520) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 520 pairs to build model! INFO @ Sat, 08 Aug 2020 12:59:14: start model_add_line... INFO @ Sat, 08 Aug 2020 12:59:14: start X-correlation... INFO @ Sat, 08 Aug 2020 12:59:14: end of X-cor INFO @ Sat, 08 Aug 2020 12:59:14: #2 finished! INFO @ Sat, 08 Aug 2020 12:59:14: #2 predicted fragment length is 204 bps INFO @ Sat, 08 Aug 2020 12:59:14: #2 alternative fragment length(s) may be 204 bps INFO @ Sat, 08 Aug 2020 12:59:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392421/SRX8392421.10_model.r WARNING @ Sat, 08 Aug 2020 12:59:14: #2 Since the d (204) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:59:14: #2 You may need to consider one of the other alternative d(s): 204 WARNING @ Sat, 08 Aug 2020 12:59:14: #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 12:59:14: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:59:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:59:14: 6000000 INFO @ Sat, 08 Aug 2020 12:59:23: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 12:59:24: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:59:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392421/SRX8392421.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:59:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392421/SRX8392421.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:59:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392421/SRX8392421.10_summits.bed INFO @ Sat, 08 Aug 2020 12:59:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (295 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:59:32: 8000000 INFO @ Sat, 08 Aug 2020 12:59:40: 9000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:59:49: 10000000 INFO @ Sat, 08 Aug 2020 12:59:57: 11000000 INFO @ Sat, 08 Aug 2020 13:00:01: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:00:01: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:00:01: #1 total tags in treatment: 4512306 INFO @ Sat, 08 Aug 2020 13:00:01: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:00:01: #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 13:00:01: #1 tags after filtering in treatment: 4147107 INFO @ Sat, 08 Aug 2020 13:00:01: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 13:00:01: #1 finished! INFO @ Sat, 08 Aug 2020 13:00:01: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:00:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:00:01: #2 number of paired peaks: 520 WARNING @ Sat, 08 Aug 2020 13:00:01: Fewer paired peaks (520) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 520 pairs to build model! INFO @ Sat, 08 Aug 2020 13:00:01: start model_add_line... INFO @ Sat, 08 Aug 2020 13:00:01: start X-correlation... INFO @ Sat, 08 Aug 2020 13:00:01: end of X-cor INFO @ Sat, 08 Aug 2020 13:00:01: #2 finished! INFO @ Sat, 08 Aug 2020 13:00:01: #2 predicted fragment length is 204 bps INFO @ Sat, 08 Aug 2020 13:00:01: #2 alternative fragment length(s) may be 204 bps INFO @ Sat, 08 Aug 2020 13:00:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392421/SRX8392421.20_model.r WARNING @ Sat, 08 Aug 2020 13:00:01: #2 Since the d (204) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:00:01: #2 You may need to consider one of the other alternative d(s): 204 WARNING @ Sat, 08 Aug 2020 13:00:01: #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 13:00:01: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:00:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:00:11: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:00:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392421/SRX8392421.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:00:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392421/SRX8392421.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:00:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392421/SRX8392421.20_summits.bed INFO @ Sat, 08 Aug 2020 13:00:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (193 records, 4 fields): 1 millis CompletedMACS2peakCalling