Job ID = 6368899 SRX = SRX6619601 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-16T00:40:00 prefetch.2.10.7: 1) Downloading 'SRR9866008'... 2020-06-16T00:40:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:48:37 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:48:37 prefetch.2.10.7: 1) 'SRR9866008' was downloaded successfully 2020-06-16T00:48:37 prefetch.2.10.7: 'SRR9866008' has 0 unresolved dependencies Read 15914497 spots for SRR9866008/SRR9866008.sra Written 15914497 spots for SRR9866008/SRR9866008.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: 00:31:16 15914497 reads; of these: 15914497 (100.00%) were paired; of these: 6889115 (43.29%) aligned concordantly 0 times 7545466 (47.41%) aligned concordantly exactly 1 time 1479916 (9.30%) aligned concordantly >1 times ---- 6889115 pairs aligned concordantly 0 times; of these: 3846684 (55.84%) aligned discordantly 1 time ---- 3042431 pairs aligned 0 times concordantly or discordantly; of these: 6084862 mates make up the pairs; of these: 4808484 (79.02%) aligned 0 times 514133 (8.45%) aligned exactly 1 time 762245 (12.53%) aligned >1 times 84.89% overall alignment rate Time searching: 00:31:16 Overall time: 00:31:16 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 20 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] 811337 / 12641245 = 0.0642 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 @ Tue, 16 Jun 2020 10:35:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6619601/SRX6619601.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6619601/SRX6619601.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6619601/SRX6619601.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6619601/SRX6619601.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 @ Tue, 16 Jun 2020 10:35:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:35:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:35:14: 1000000 INFO @ Tue, 16 Jun 2020 10:35:26: 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 @ Tue, 16 Jun 2020 10:35:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6619601/SRX6619601.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6619601/SRX6619601.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6619601/SRX6619601.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6619601/SRX6619601.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 @ Tue, 16 Jun 2020 10:35:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:35:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:35:38: 3000000 INFO @ Tue, 16 Jun 2020 10:35:45: 1000000 INFO @ Tue, 16 Jun 2020 10:35:51: 4000000 INFO @ Tue, 16 Jun 2020 10:35:58: 2000000 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 @ Tue, 16 Jun 2020 10:36:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6619601/SRX6619601.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6619601/SRX6619601.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6619601/SRX6619601.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6619601/SRX6619601.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 @ Tue, 16 Jun 2020 10:36:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:36:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:36:03: 5000000 INFO @ Tue, 16 Jun 2020 10:36:10: 3000000 INFO @ Tue, 16 Jun 2020 10:36:15: 6000000 INFO @ Tue, 16 Jun 2020 10:36:16: 1000000 INFO @ Tue, 16 Jun 2020 10:36:23: 4000000 INFO @ Tue, 16 Jun 2020 10:36:27: 7000000 INFO @ Tue, 16 Jun 2020 10:36:28: 2000000 INFO @ Tue, 16 Jun 2020 10:36:36: 5000000 INFO @ Tue, 16 Jun 2020 10:36:39: 8000000 INFO @ Tue, 16 Jun 2020 10:36:41: 3000000 INFO @ Tue, 16 Jun 2020 10:36:50: 6000000 INFO @ Tue, 16 Jun 2020 10:36:52: 9000000 INFO @ Tue, 16 Jun 2020 10:36:53: 4000000 INFO @ Tue, 16 Jun 2020 10:37:03: 7000000 INFO @ Tue, 16 Jun 2020 10:37:04: 10000000 INFO @ Tue, 16 Jun 2020 10:37:06: 5000000 INFO @ Tue, 16 Jun 2020 10:37:16: 11000000 INFO @ Tue, 16 Jun 2020 10:37:18: 8000000 INFO @ Tue, 16 Jun 2020 10:37:19: 6000000 INFO @ Tue, 16 Jun 2020 10:37:30: 12000000 INFO @ Tue, 16 Jun 2020 10:37:32: 9000000 INFO @ Tue, 16 Jun 2020 10:37:33: 7000000 INFO @ Tue, 16 Jun 2020 10:37:43: 13000000 INFO @ Tue, 16 Jun 2020 10:37:46: 10000000 INFO @ Tue, 16 Jun 2020 10:37:47: 8000000 INFO @ Tue, 16 Jun 2020 10:37:56: 14000000 INFO @ Tue, 16 Jun 2020 10:37:58: 11000000 INFO @ Tue, 16 Jun 2020 10:38:01: 9000000 INFO @ Tue, 16 Jun 2020 10:38:09: 15000000 INFO @ Tue, 16 Jun 2020 10:38:10: 12000000 INFO @ Tue, 16 Jun 2020 10:38:14: 10000000 INFO @ Tue, 16 Jun 2020 10:38:23: 16000000 INFO @ Tue, 16 Jun 2020 10:38:23: 13000000 INFO @ Tue, 16 Jun 2020 10:38:27: 11000000 INFO @ Tue, 16 Jun 2020 10:38:35: 17000000 INFO @ Tue, 16 Jun 2020 10:38:35: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:38:39: 12000000 INFO @ Tue, 16 Jun 2020 10:38:47: 18000000 INFO @ Tue, 16 Jun 2020 10:38:48: 15000000 INFO @ Tue, 16 Jun 2020 10:38:52: 13000000 INFO @ Tue, 16 Jun 2020 10:39:00: 16000000 INFO @ Tue, 16 Jun 2020 10:39:01: 19000000 INFO @ Tue, 16 Jun 2020 10:39:04: 14000000 INFO @ Tue, 16 Jun 2020 10:39:13: 17000000 INFO @ Tue, 16 Jun 2020 10:39:14: 20000000 INFO @ Tue, 16 Jun 2020 10:39:16: 15000000 INFO @ Tue, 16 Jun 2020 10:39:27: 18000000 INFO @ Tue, 16 Jun 2020 10:39:27: 21000000 INFO @ Tue, 16 Jun 2020 10:39:28: 16000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:39:39: 19000000 INFO @ Tue, 16 Jun 2020 10:39:41: 22000000 INFO @ Tue, 16 Jun 2020 10:39:41: 17000000 INFO @ Tue, 16 Jun 2020 10:39:51: 20000000 INFO @ Tue, 16 Jun 2020 10:39:54: 23000000 INFO @ Tue, 16 Jun 2020 10:39:55: 18000000 INFO @ Tue, 16 Jun 2020 10:40:03: 21000000 INFO @ Tue, 16 Jun 2020 10:40:07: 19000000 INFO @ Tue, 16 Jun 2020 10:40:07: 24000000 INFO @ Tue, 16 Jun 2020 10:40:16: 22000000 INFO @ Tue, 16 Jun 2020 10:40:20: 20000000 INFO @ Tue, 16 Jun 2020 10:40:21: 25000000 INFO @ Tue, 16 Jun 2020 10:40:26: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 10:40:26: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 10:40:26: #1 total tags in treatment: 8419111 INFO @ Tue, 16 Jun 2020 10:40:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:40:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 10:40:26: #1 tags after filtering in treatment: 7503238 INFO @ Tue, 16 Jun 2020 10:40:26: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 16 Jun 2020 10:40:26: #1 finished! INFO @ Tue, 16 Jun 2020 10:40:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:40:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:40:27: #2 number of paired peaks: 310 WARNING @ Tue, 16 Jun 2020 10:40:27: Fewer paired peaks (310) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 310 pairs to build model! INFO @ Tue, 16 Jun 2020 10:40:27: start model_add_line... INFO @ Tue, 16 Jun 2020 10:40:27: start X-correlation... INFO @ Tue, 16 Jun 2020 10:40:27: end of X-cor INFO @ Tue, 16 Jun 2020 10:40:27: #2 finished! INFO @ Tue, 16 Jun 2020 10:40:27: #2 predicted fragment length is 200 bps INFO @ Tue, 16 Jun 2020 10:40:27: #2 alternative fragment length(s) may be 200 bps INFO @ Tue, 16 Jun 2020 10:40:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6619601/SRX6619601.05_model.r WARNING @ Tue, 16 Jun 2020 10:40:27: #2 Since the d (200) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:40:27: #2 You may need to consider one of the other alternative d(s): 200 WARNING @ Tue, 16 Jun 2020 10:40:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 10:40:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:40:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:40:28: 23000000 INFO @ Tue, 16 Jun 2020 10:40:32: 21000000 INFO @ Tue, 16 Jun 2020 10:40:40: 24000000 INFO @ Tue, 16 Jun 2020 10:40:43: 22000000 INFO @ Tue, 16 Jun 2020 10:40:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:40:51: 25000000 INFO @ Tue, 16 Jun 2020 10:40:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6619601/SRX6619601.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:40:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6619601/SRX6619601.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:40:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6619601/SRX6619601.05_summits.bed INFO @ Tue, 16 Jun 2020 10:40:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (394 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:40:55: 23000000 INFO @ Tue, 16 Jun 2020 10:40:55: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 10:40:55: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 10:40:55: #1 total tags in treatment: 8419111 INFO @ Tue, 16 Jun 2020 10:40:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:40:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 10:40:56: #1 tags after filtering in treatment: 7503238 INFO @ Tue, 16 Jun 2020 10:40:56: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 16 Jun 2020 10:40:56: #1 finished! INFO @ Tue, 16 Jun 2020 10:40:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:40:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:40:56: #2 number of paired peaks: 310 WARNING @ Tue, 16 Jun 2020 10:40:56: Fewer paired peaks (310) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 310 pairs to build model! INFO @ Tue, 16 Jun 2020 10:40:56: start model_add_line... INFO @ Tue, 16 Jun 2020 10:40:56: start X-correlation... INFO @ Tue, 16 Jun 2020 10:40:56: end of X-cor INFO @ Tue, 16 Jun 2020 10:40:56: #2 finished! INFO @ Tue, 16 Jun 2020 10:40:56: #2 predicted fragment length is 200 bps INFO @ Tue, 16 Jun 2020 10:40:56: #2 alternative fragment length(s) may be 200 bps INFO @ Tue, 16 Jun 2020 10:40:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6619601/SRX6619601.10_model.r WARNING @ Tue, 16 Jun 2020 10:40:56: #2 Since the d (200) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:40:56: #2 You may need to consider one of the other alternative d(s): 200 WARNING @ Tue, 16 Jun 2020 10:40:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 10:40:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:40:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:41:05: 24000000 INFO @ Tue, 16 Jun 2020 10:41:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:41:14: 25000000 INFO @ Tue, 16 Jun 2020 10:41:18: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 10:41:18: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 10:41:18: #1 total tags in treatment: 8419111 INFO @ Tue, 16 Jun 2020 10:41:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:41:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 10:41:18: #1 tags after filtering in treatment: 7503238 INFO @ Tue, 16 Jun 2020 10:41:18: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 16 Jun 2020 10:41:18: #1 finished! INFO @ Tue, 16 Jun 2020 10:41:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:41:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:41:18: #2 number of paired peaks: 310 WARNING @ Tue, 16 Jun 2020 10:41:18: Fewer paired peaks (310) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 310 pairs to build model! INFO @ Tue, 16 Jun 2020 10:41:18: start model_add_line... INFO @ Tue, 16 Jun 2020 10:41:18: start X-correlation... INFO @ Tue, 16 Jun 2020 10:41:18: end of X-cor INFO @ Tue, 16 Jun 2020 10:41:18: #2 finished! INFO @ Tue, 16 Jun 2020 10:41:18: #2 predicted fragment length is 200 bps INFO @ Tue, 16 Jun 2020 10:41:18: #2 alternative fragment length(s) may be 200 bps INFO @ Tue, 16 Jun 2020 10:41:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6619601/SRX6619601.20_model.r WARNING @ Tue, 16 Jun 2020 10:41:18: #2 Since the d (200) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:41:18: #2 You may need to consider one of the other alternative d(s): 200 WARNING @ Tue, 16 Jun 2020 10:41:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 10:41:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:41:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:41:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6619601/SRX6619601.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:41:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6619601/SRX6619601.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:41:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6619601/SRX6619601.10_summits.bed INFO @ Tue, 16 Jun 2020 10:41:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (272 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:41:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:41:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6619601/SRX6619601.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:41:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6619601/SRX6619601.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:41:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6619601/SRX6619601.20_summits.bed INFO @ Tue, 16 Jun 2020 10:41:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (179 records, 4 fields): 2 millis CompletedMACS2peakCalling