Job ID = 14158016 SRX = SRX10641213 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-08T04:51:25 prefetch.2.10.7: 1) Downloading 'SRR14280065'... 2021-12-08T04:51:25 prefetch.2.10.7: Downloading via HTTPS... 2021-12-08T04:53:30 prefetch.2.10.7: HTTPS download succeed 2021-12-08T04:53:30 prefetch.2.10.7: 1) 'SRR14280065' was downloaded successfully 2021-12-08T04:53:30 prefetch.2.10.7: 'SRR14280065' has 0 unresolved dependencies Read 15590980 spots for SRR14280065/SRR14280065.sra Written 15590980 spots for SRR14280065/SRR14280065.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158307 ("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: 00:22:19 15590980 reads; of these: 15590980 (100.00%) were paired; of these: 9433991 (60.51%) aligned concordantly 0 times 5104602 (32.74%) aligned concordantly exactly 1 time 1052387 (6.75%) aligned concordantly >1 times ---- 9433991 pairs aligned concordantly 0 times; of these: 2523828 (26.75%) aligned discordantly 1 time ---- 6910163 pairs aligned 0 times concordantly or discordantly; of these: 13820326 mates make up the pairs; of these: 12628919 (91.38%) aligned 0 times 647114 (4.68%) aligned exactly 1 time 544293 (3.94%) aligned >1 times 59.50% overall alignment rate Time searching: 00:22:20 Overall time: 00:22:20 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 16 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] 1181002 / 8638592 = 0.1367 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 14:27:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641213/SRX10641213.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641213/SRX10641213.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641213/SRX10641213.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641213/SRX10641213.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 @ Wed, 08 Dec 2021 14:27:14: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:27:14: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:27:22: 1000000 INFO @ Wed, 08 Dec 2021 14:27:30: 2000000 INFO @ Wed, 08 Dec 2021 14:27:37: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 14:27:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641213/SRX10641213.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641213/SRX10641213.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641213/SRX10641213.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641213/SRX10641213.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 @ Wed, 08 Dec 2021 14:27:43: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:27:43: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:27:46: 4000000 INFO @ Wed, 08 Dec 2021 14:27:54: 1000000 INFO @ Wed, 08 Dec 2021 14:27:56: 5000000 INFO @ Wed, 08 Dec 2021 14:28:05: 2000000 INFO @ Wed, 08 Dec 2021 14:28:06: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 14:28:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641213/SRX10641213.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641213/SRX10641213.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641213/SRX10641213.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641213/SRX10641213.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 @ Wed, 08 Dec 2021 14:28:13: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:28:13: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:28:16: 3000000 INFO @ Wed, 08 Dec 2021 14:28:17: 7000000 INFO @ Wed, 08 Dec 2021 14:28:25: 1000000 INFO @ Wed, 08 Dec 2021 14:28:27: 8000000 INFO @ Wed, 08 Dec 2021 14:28:28: 4000000 INFO @ Wed, 08 Dec 2021 14:28:37: 2000000 INFO @ Wed, 08 Dec 2021 14:28:37: 9000000 INFO @ Wed, 08 Dec 2021 14:28:39: 5000000 INFO @ Wed, 08 Dec 2021 14:28:48: 10000000 INFO @ Wed, 08 Dec 2021 14:28:49: 3000000 INFO @ Wed, 08 Dec 2021 14:28:50: 6000000 INFO @ Wed, 08 Dec 2021 14:28:58: 11000000 INFO @ Wed, 08 Dec 2021 14:29:01: 7000000 INFO @ Wed, 08 Dec 2021 14:29:01: 4000000 INFO @ Wed, 08 Dec 2021 14:29:09: 12000000 INFO @ Wed, 08 Dec 2021 14:29:12: 8000000 INFO @ Wed, 08 Dec 2021 14:29:13: 5000000 INFO @ Wed, 08 Dec 2021 14:29:19: 13000000 INFO @ Wed, 08 Dec 2021 14:29:23: 9000000 INFO @ Wed, 08 Dec 2021 14:29:26: 6000000 INFO @ Wed, 08 Dec 2021 14:29:30: 14000000 INFO @ Wed, 08 Dec 2021 14:29:34: 10000000 INFO @ Wed, 08 Dec 2021 14:29:38: 7000000 INFO @ Wed, 08 Dec 2021 14:29:40: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 14:29:45: 11000000 INFO @ Wed, 08 Dec 2021 14:29:50: 8000000 INFO @ Wed, 08 Dec 2021 14:29:50: 16000000 INFO @ Wed, 08 Dec 2021 14:29:52: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 14:29:52: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 14:29:52: #1 total tags in treatment: 5249283 INFO @ Wed, 08 Dec 2021 14:29:52: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:29:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 14:29:53: #1 tags after filtering in treatment: 4785996 INFO @ Wed, 08 Dec 2021 14:29:53: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 08 Dec 2021 14:29:53: #1 finished! INFO @ Wed, 08 Dec 2021 14:29:53: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:29:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:29:53: #2 number of paired peaks: 610 WARNING @ Wed, 08 Dec 2021 14:29:53: Fewer paired peaks (610) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 610 pairs to build model! INFO @ Wed, 08 Dec 2021 14:29:53: start model_add_line... INFO @ Wed, 08 Dec 2021 14:29:53: start X-correlation... INFO @ Wed, 08 Dec 2021 14:29:53: end of X-cor INFO @ Wed, 08 Dec 2021 14:29:53: #2 finished! INFO @ Wed, 08 Dec 2021 14:29:53: #2 predicted fragment length is 216 bps INFO @ Wed, 08 Dec 2021 14:29:53: #2 alternative fragment length(s) may be 216 bps INFO @ Wed, 08 Dec 2021 14:29:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641213/SRX10641213.05_model.r WARNING @ Wed, 08 Dec 2021 14:29:53: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:29:53: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Wed, 08 Dec 2021 14:29:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 14:29:53: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:29:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:29:57: 12000000 INFO @ Wed, 08 Dec 2021 14:30:02: 9000000 INFO @ Wed, 08 Dec 2021 14:30:05: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:30:07: 13000000 INFO @ Wed, 08 Dec 2021 14:30:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641213/SRX10641213.05_peaks.xls INFO @ Wed, 08 Dec 2021 14:30:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641213/SRX10641213.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:30:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641213/SRX10641213.05_summits.bed INFO @ Wed, 08 Dec 2021 14:30:10: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (408 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:30:14: 10000000 INFO @ Wed, 08 Dec 2021 14:30:18: 14000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 14:30:25: 11000000 INFO @ Wed, 08 Dec 2021 14:30:29: 15000000 INFO @ Wed, 08 Dec 2021 14:30:37: 12000000 INFO @ Wed, 08 Dec 2021 14:30:40: 16000000 INFO @ Wed, 08 Dec 2021 14:30:42: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 14:30:42: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 14:30:42: #1 total tags in treatment: 5249283 INFO @ Wed, 08 Dec 2021 14:30:42: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:30:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 14:30:42: #1 tags after filtering in treatment: 4785996 INFO @ Wed, 08 Dec 2021 14:30:42: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 08 Dec 2021 14:30:42: #1 finished! INFO @ Wed, 08 Dec 2021 14:30:42: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:30:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:30:43: #2 number of paired peaks: 610 WARNING @ Wed, 08 Dec 2021 14:30:43: Fewer paired peaks (610) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 610 pairs to build model! INFO @ Wed, 08 Dec 2021 14:30:43: start model_add_line... INFO @ Wed, 08 Dec 2021 14:30:43: start X-correlation... INFO @ Wed, 08 Dec 2021 14:30:43: end of X-cor INFO @ Wed, 08 Dec 2021 14:30:43: #2 finished! INFO @ Wed, 08 Dec 2021 14:30:43: #2 predicted fragment length is 216 bps INFO @ Wed, 08 Dec 2021 14:30:43: #2 alternative fragment length(s) may be 216 bps INFO @ Wed, 08 Dec 2021 14:30:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641213/SRX10641213.10_model.r WARNING @ Wed, 08 Dec 2021 14:30:43: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:30:43: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Wed, 08 Dec 2021 14:30:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 14:30:43: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:30:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:30:48: 13000000 INFO @ Wed, 08 Dec 2021 14:30:54: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:30:59: 14000000 INFO @ Wed, 08 Dec 2021 14:30:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641213/SRX10641213.10_peaks.xls INFO @ Wed, 08 Dec 2021 14:30:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641213/SRX10641213.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:30:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641213/SRX10641213.10_summits.bed INFO @ Wed, 08 Dec 2021 14:30:59: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (322 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:31:10: 15000000 INFO @ Wed, 08 Dec 2021 14:31:20: 16000000 INFO @ Wed, 08 Dec 2021 14:31:22: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 14:31:22: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 14:31:22: #1 total tags in treatment: 5249283 INFO @ Wed, 08 Dec 2021 14:31:22: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:31:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 14:31:22: #1 tags after filtering in treatment: 4785996 INFO @ Wed, 08 Dec 2021 14:31:22: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 08 Dec 2021 14:31:22: #1 finished! INFO @ Wed, 08 Dec 2021 14:31:22: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:31:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:31:22: #2 number of paired peaks: 610 WARNING @ Wed, 08 Dec 2021 14:31:22: Fewer paired peaks (610) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 610 pairs to build model! INFO @ Wed, 08 Dec 2021 14:31:22: start model_add_line... INFO @ Wed, 08 Dec 2021 14:31:22: start X-correlation... INFO @ Wed, 08 Dec 2021 14:31:23: end of X-cor INFO @ Wed, 08 Dec 2021 14:31:23: #2 finished! INFO @ Wed, 08 Dec 2021 14:31:23: #2 predicted fragment length is 216 bps INFO @ Wed, 08 Dec 2021 14:31:23: #2 alternative fragment length(s) may be 216 bps INFO @ Wed, 08 Dec 2021 14:31:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641213/SRX10641213.20_model.r WARNING @ Wed, 08 Dec 2021 14:31:23: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:31:23: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Wed, 08 Dec 2021 14:31:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 14:31:23: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:31:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:31:34: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:31:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641213/SRX10641213.20_peaks.xls INFO @ Wed, 08 Dec 2021 14:31:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641213/SRX10641213.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:31:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641213/SRX10641213.20_summits.bed INFO @ Wed, 08 Dec 2021 14:31:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (227 records, 4 fields): 1 millis CompletedMACS2peakCalling