Job ID = 6368867 SRX = SRX6619565 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-16T00:39:19 prefetch.2.10.7: 1) Downloading 'SRR9866044'... 2020-06-16T00:39:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:49:14 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:49:14 prefetch.2.10.7: 1) 'SRR9866044' was downloaded successfully 2020-06-16T00:49:14 prefetch.2.10.7: 'SRR9866044' has 0 unresolved dependencies Read 16295947 spots for SRR9866044/SRR9866044.sra Written 16295947 spots for SRR9866044/SRR9866044.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: 00:34:24 16295947 reads; of these: 16295947 (100.00%) were paired; of these: 6011907 (36.89%) aligned concordantly 0 times 8680595 (53.27%) aligned concordantly exactly 1 time 1603445 (9.84%) aligned concordantly >1 times ---- 6011907 pairs aligned concordantly 0 times; of these: 3667834 (61.01%) aligned discordantly 1 time ---- 2344073 pairs aligned 0 times concordantly or discordantly; of these: 4688146 mates make up the pairs; of these: 3427122 (73.10%) aligned 0 times 533718 (11.38%) aligned exactly 1 time 727306 (15.51%) aligned >1 times 89.48% overall alignment rate Time searching: 00:34:24 Overall time: 00:34:24 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 24 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] 900686 / 13709888 = 0.0657 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 10:40:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6619565/SRX6619565.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6619565/SRX6619565.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6619565/SRX6619565.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6619565/SRX6619565.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 10:40:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:40:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:41:05: 1000000 INFO @ Tue, 16 Jun 2020 10:41:14: 2000000 INFO @ Tue, 16 Jun 2020 10:41:23: 3000000 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 10:41:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6619565/SRX6619565.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6619565/SRX6619565.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6619565/SRX6619565.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6619565/SRX6619565.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 10:41:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:41:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:41:33: 4000000 INFO @ Tue, 16 Jun 2020 10:41:37: 1000000 INFO @ Tue, 16 Jun 2020 10:41:42: 5000000 INFO @ Tue, 16 Jun 2020 10:41:47: 2000000 INFO @ Tue, 16 Jun 2020 10:41:52: 6000000 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 10:41:56: 3000000 INFO @ Tue, 16 Jun 2020 10:41:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6619565/SRX6619565.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6619565/SRX6619565.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6619565/SRX6619565.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6619565/SRX6619565.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 10:41:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:41:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:42:02: 7000000 INFO @ Tue, 16 Jun 2020 10:42:06: 4000000 INFO @ Tue, 16 Jun 2020 10:42:08: 1000000 INFO @ Tue, 16 Jun 2020 10:42:13: 8000000 INFO @ Tue, 16 Jun 2020 10:42:16: 5000000 INFO @ Tue, 16 Jun 2020 10:42:19: 2000000 INFO @ Tue, 16 Jun 2020 10:42:24: 9000000 INFO @ Tue, 16 Jun 2020 10:42:26: 6000000 INFO @ Tue, 16 Jun 2020 10:42:30: 3000000 INFO @ Tue, 16 Jun 2020 10:42:35: 10000000 INFO @ Tue, 16 Jun 2020 10:42:36: 7000000 INFO @ Tue, 16 Jun 2020 10:42:42: 4000000 INFO @ Tue, 16 Jun 2020 10:42:45: 11000000 INFO @ Tue, 16 Jun 2020 10:42:47: 8000000 INFO @ Tue, 16 Jun 2020 10:42:53: 5000000 INFO @ Tue, 16 Jun 2020 10:42:56: 12000000 INFO @ Tue, 16 Jun 2020 10:42:57: 9000000 INFO @ Tue, 16 Jun 2020 10:43:05: 6000000 INFO @ Tue, 16 Jun 2020 10:43:06: 13000000 INFO @ Tue, 16 Jun 2020 10:43:07: 10000000 INFO @ Tue, 16 Jun 2020 10:43:16: 7000000 INFO @ Tue, 16 Jun 2020 10:43:17: 14000000 INFO @ Tue, 16 Jun 2020 10:43:17: 11000000 INFO @ Tue, 16 Jun 2020 10:43:27: 15000000 INFO @ Tue, 16 Jun 2020 10:43:27: 8000000 INFO @ Tue, 16 Jun 2020 10:43:28: 12000000 INFO @ Tue, 16 Jun 2020 10:43:37: 16000000 INFO @ Tue, 16 Jun 2020 10:43:38: 13000000 INFO @ Tue, 16 Jun 2020 10:43:38: 9000000 INFO @ Tue, 16 Jun 2020 10:43:48: 17000000 INFO @ Tue, 16 Jun 2020 10:43:48: 14000000 INFO @ Tue, 16 Jun 2020 10:43:50: 10000000 INFO @ Tue, 16 Jun 2020 10:43:58: 18000000 INFO @ Tue, 16 Jun 2020 10:43:58: 15000000 INFO @ Tue, 16 Jun 2020 10:44:01: 11000000 INFO @ Tue, 16 Jun 2020 10:44:08: 16000000 INFO @ Tue, 16 Jun 2020 10:44:08: 19000000 INFO @ Tue, 16 Jun 2020 10:44:12: 12000000 INFO @ Tue, 16 Jun 2020 10:44:18: 17000000 INFO @ Tue, 16 Jun 2020 10:44:18: 20000000 INFO @ Tue, 16 Jun 2020 10:44:24: 13000000 INFO @ Tue, 16 Jun 2020 10:44:28: 18000000 INFO @ Tue, 16 Jun 2020 10:44:28: 21000000 INFO @ Tue, 16 Jun 2020 10:44:35: 14000000 INFO @ Tue, 16 Jun 2020 10:44:38: 19000000 INFO @ Tue, 16 Jun 2020 10:44:38: 22000000 INFO @ Tue, 16 Jun 2020 10:44:47: 15000000 INFO @ Tue, 16 Jun 2020 10:44:48: 20000000 INFO @ Tue, 16 Jun 2020 10:44:48: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:44:57: 21000000 INFO @ Tue, 16 Jun 2020 10:44:58: 24000000 INFO @ Tue, 16 Jun 2020 10:44:58: 16000000 INFO @ Tue, 16 Jun 2020 10:45:07: 22000000 INFO @ Tue, 16 Jun 2020 10:45:08: 25000000 INFO @ Tue, 16 Jun 2020 10:45:10: 17000000 INFO @ Tue, 16 Jun 2020 10:45:17: 23000000 INFO @ Tue, 16 Jun 2020 10:45:18: 26000000 INFO @ Tue, 16 Jun 2020 10:45:21: 18000000 INFO @ Tue, 16 Jun 2020 10:45:27: 24000000 INFO @ Tue, 16 Jun 2020 10:45:28: 27000000 INFO @ Tue, 16 Jun 2020 10:45:31: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 10:45:31: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 10:45:31: #1 total tags in treatment: 9583224 INFO @ Tue, 16 Jun 2020 10:45:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:45:31: #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 10:45:31: #1 tags after filtering in treatment: 8567283 INFO @ Tue, 16 Jun 2020 10:45:31: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 16 Jun 2020 10:45:31: #1 finished! INFO @ Tue, 16 Jun 2020 10:45:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:45:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:45:32: #2 number of paired peaks: 284 WARNING @ Tue, 16 Jun 2020 10:45:32: Fewer paired peaks (284) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 284 pairs to build model! INFO @ Tue, 16 Jun 2020 10:45:32: start model_add_line... INFO @ Tue, 16 Jun 2020 10:45:32: start X-correlation... INFO @ Tue, 16 Jun 2020 10:45:32: end of X-cor INFO @ Tue, 16 Jun 2020 10:45:32: #2 finished! INFO @ Tue, 16 Jun 2020 10:45:32: #2 predicted fragment length is 216 bps INFO @ Tue, 16 Jun 2020 10:45:32: #2 alternative fragment length(s) may be 210,216 bps INFO @ Tue, 16 Jun 2020 10:45:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6619565/SRX6619565.05_model.r WARNING @ Tue, 16 Jun 2020 10:45:32: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:45:32: #2 You may need to consider one of the other alternative d(s): 210,216 WARNING @ Tue, 16 Jun 2020 10:45:32: #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 10:45:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:45:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:45:32: 19000000 INFO @ Tue, 16 Jun 2020 10:45:37: 25000000 INFO @ Tue, 16 Jun 2020 10:45:44: 20000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:45:46: 26000000 INFO @ Tue, 16 Jun 2020 10:45:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:45:55: 21000000 INFO @ Tue, 16 Jun 2020 10:45:56: 27000000 INFO @ Tue, 16 Jun 2020 10:46:00: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 10:46:00: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 10:46:00: #1 total tags in treatment: 9583224 INFO @ Tue, 16 Jun 2020 10:46:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:46:00: #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 10:46:00: #1 tags after filtering in treatment: 8567283 INFO @ Tue, 16 Jun 2020 10:46:00: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 16 Jun 2020 10:46:00: #1 finished! INFO @ Tue, 16 Jun 2020 10:46:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:46:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:46:00: #2 number of paired peaks: 284 WARNING @ Tue, 16 Jun 2020 10:46:00: Fewer paired peaks (284) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 284 pairs to build model! INFO @ Tue, 16 Jun 2020 10:46:00: start model_add_line... INFO @ Tue, 16 Jun 2020 10:46:00: start X-correlation... INFO @ Tue, 16 Jun 2020 10:46:00: end of X-cor INFO @ Tue, 16 Jun 2020 10:46:00: #2 finished! INFO @ Tue, 16 Jun 2020 10:46:00: #2 predicted fragment length is 216 bps INFO @ Tue, 16 Jun 2020 10:46:00: #2 alternative fragment length(s) may be 210,216 bps INFO @ Tue, 16 Jun 2020 10:46:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6619565/SRX6619565.10_model.r WARNING @ Tue, 16 Jun 2020 10:46:00: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:46:00: #2 You may need to consider one of the other alternative d(s): 210,216 WARNING @ Tue, 16 Jun 2020 10:46:00: #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 10:46:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:46:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:46:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6619565/SRX6619565.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:46:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6619565/SRX6619565.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:46:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6619565/SRX6619565.05_summits.bed INFO @ Tue, 16 Jun 2020 10:46:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (373 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:46:06: 22000000 INFO @ Tue, 16 Jun 2020 10:46:16: 23000000 INFO @ Tue, 16 Jun 2020 10:46:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:46:27: 24000000 INFO @ Tue, 16 Jun 2020 10:46:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6619565/SRX6619565.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:46:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6619565/SRX6619565.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:46:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6619565/SRX6619565.10_summits.bed INFO @ Tue, 16 Jun 2020 10:46:32: 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 10:46:37: 25000000 INFO @ Tue, 16 Jun 2020 10:46:47: 26000000 INFO @ Tue, 16 Jun 2020 10:46:57: 27000000 INFO @ Tue, 16 Jun 2020 10:47:01: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 10:47:01: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 10:47:01: #1 total tags in treatment: 9583224 INFO @ Tue, 16 Jun 2020 10:47:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:47:01: #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 10:47:01: #1 tags after filtering in treatment: 8567283 INFO @ Tue, 16 Jun 2020 10:47:01: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 16 Jun 2020 10:47:01: #1 finished! INFO @ Tue, 16 Jun 2020 10:47:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:47:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:47:02: #2 number of paired peaks: 284 WARNING @ Tue, 16 Jun 2020 10:47:02: Fewer paired peaks (284) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 284 pairs to build model! INFO @ Tue, 16 Jun 2020 10:47:02: start model_add_line... INFO @ Tue, 16 Jun 2020 10:47:02: start X-correlation... INFO @ Tue, 16 Jun 2020 10:47:02: end of X-cor INFO @ Tue, 16 Jun 2020 10:47:02: #2 finished! INFO @ Tue, 16 Jun 2020 10:47:02: #2 predicted fragment length is 216 bps INFO @ Tue, 16 Jun 2020 10:47:02: #2 alternative fragment length(s) may be 210,216 bps INFO @ Tue, 16 Jun 2020 10:47:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6619565/SRX6619565.20_model.r WARNING @ Tue, 16 Jun 2020 10:47:02: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:47:02: #2 You may need to consider one of the other alternative d(s): 210,216 WARNING @ Tue, 16 Jun 2020 10:47:02: #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 10:47:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:47:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:47:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:47:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6619565/SRX6619565.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:47:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6619565/SRX6619565.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:47:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6619565/SRX6619565.20_summits.bed INFO @ Tue, 16 Jun 2020 10:47:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (174 records, 4 fields): 1 millis CompletedMACS2peakCalling