Job ID = 6367802 SRX = SRX4085370 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:35:20 prefetch.2.10.7: 1) Downloading 'SRR7167399'... 2020-06-15T23:35:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:47:12 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:47:12 prefetch.2.10.7: 1) 'SRR7167399' was downloaded successfully Read 21514033 spots for SRR7167399/SRR7167399.sra Written 21514033 spots for SRR7167399/SRR7167399.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: 00:13:50 21514033 reads; of these: 21514033 (100.00%) were paired; of these: 7543298 (35.06%) aligned concordantly 0 times 12319010 (57.26%) aligned concordantly exactly 1 time 1651725 (7.68%) aligned concordantly >1 times ---- 7543298 pairs aligned concordantly 0 times; of these: 366250 (4.86%) aligned discordantly 1 time ---- 7177048 pairs aligned 0 times concordantly or discordantly; of these: 14354096 mates make up the pairs; of these: 11345946 (79.04%) aligned 0 times 2636276 (18.37%) aligned exactly 1 time 371874 (2.59%) aligned >1 times 73.63% overall alignment rate Time searching: 00:13:50 Overall time: 00:13:50 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] 968016 / 14222990 = 0.0681 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 09:12:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085370/SRX4085370.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085370/SRX4085370.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085370/SRX4085370.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085370/SRX4085370.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 09:12:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:12:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:12:30: 1000000 INFO @ Tue, 16 Jun 2020 09:12:36: 2000000 INFO @ Tue, 16 Jun 2020 09:12:43: 3000000 INFO @ Tue, 16 Jun 2020 09:12:49: 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 @ Tue, 16 Jun 2020 09:12:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085370/SRX4085370.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085370/SRX4085370.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085370/SRX4085370.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085370/SRX4085370.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 09:12:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:12:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:12:56: 5000000 INFO @ Tue, 16 Jun 2020 09:13:00: 1000000 INFO @ Tue, 16 Jun 2020 09:13:03: 6000000 INFO @ Tue, 16 Jun 2020 09:13:07: 2000000 INFO @ Tue, 16 Jun 2020 09:13:10: 7000000 INFO @ Tue, 16 Jun 2020 09:13:15: 3000000 INFO @ Tue, 16 Jun 2020 09:13:17: 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 @ Tue, 16 Jun 2020 09:13:22: 4000000 INFO @ Tue, 16 Jun 2020 09:13:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085370/SRX4085370.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085370/SRX4085370.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085370/SRX4085370.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085370/SRX4085370.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 09:13:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:13:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:13:25: 9000000 INFO @ Tue, 16 Jun 2020 09:13:30: 5000000 INFO @ Tue, 16 Jun 2020 09:13:31: 1000000 INFO @ Tue, 16 Jun 2020 09:13:32: 10000000 INFO @ Tue, 16 Jun 2020 09:13:37: 6000000 INFO @ Tue, 16 Jun 2020 09:13:38: 2000000 INFO @ Tue, 16 Jun 2020 09:13:40: 11000000 INFO @ Tue, 16 Jun 2020 09:13:45: 7000000 INFO @ Tue, 16 Jun 2020 09:13:46: 3000000 INFO @ Tue, 16 Jun 2020 09:13:47: 12000000 INFO @ Tue, 16 Jun 2020 09:13:52: 8000000 INFO @ Tue, 16 Jun 2020 09:13:54: 4000000 INFO @ Tue, 16 Jun 2020 09:13:55: 13000000 INFO @ Tue, 16 Jun 2020 09:14:00: 9000000 INFO @ Tue, 16 Jun 2020 09:14:02: 5000000 INFO @ Tue, 16 Jun 2020 09:14:03: 14000000 INFO @ Tue, 16 Jun 2020 09:14:08: 10000000 INFO @ Tue, 16 Jun 2020 09:14:10: 6000000 INFO @ Tue, 16 Jun 2020 09:14:10: 15000000 INFO @ Tue, 16 Jun 2020 09:14:15: 11000000 INFO @ Tue, 16 Jun 2020 09:14:17: 7000000 INFO @ Tue, 16 Jun 2020 09:14:18: 16000000 INFO @ Tue, 16 Jun 2020 09:14:23: 12000000 INFO @ Tue, 16 Jun 2020 09:14:25: 8000000 INFO @ Tue, 16 Jun 2020 09:14:25: 17000000 INFO @ Tue, 16 Jun 2020 09:14:30: 13000000 INFO @ Tue, 16 Jun 2020 09:14:32: 9000000 INFO @ Tue, 16 Jun 2020 09:14:33: 18000000 INFO @ Tue, 16 Jun 2020 09:14:38: 14000000 INFO @ Tue, 16 Jun 2020 09:14:40: 10000000 INFO @ Tue, 16 Jun 2020 09:14:41: 19000000 INFO @ Tue, 16 Jun 2020 09:14:46: 15000000 INFO @ Tue, 16 Jun 2020 09:14:48: 11000000 INFO @ Tue, 16 Jun 2020 09:14:48: 20000000 INFO @ Tue, 16 Jun 2020 09:14:53: 16000000 INFO @ Tue, 16 Jun 2020 09:14:56: 12000000 INFO @ Tue, 16 Jun 2020 09:14:56: 21000000 INFO @ Tue, 16 Jun 2020 09:15:01: 17000000 INFO @ Tue, 16 Jun 2020 09:15:03: 22000000 INFO @ Tue, 16 Jun 2020 09:15:04: 13000000 INFO @ Tue, 16 Jun 2020 09:15:08: 18000000 INFO @ Tue, 16 Jun 2020 09:15:11: 23000000 INFO @ Tue, 16 Jun 2020 09:15:11: 14000000 INFO @ Tue, 16 Jun 2020 09:15:16: 19000000 INFO @ Tue, 16 Jun 2020 09:15:19: 24000000 INFO @ Tue, 16 Jun 2020 09:15:19: 15000000 INFO @ Tue, 16 Jun 2020 09:15:24: 20000000 INFO @ Tue, 16 Jun 2020 09:15:26: 25000000 INFO @ Tue, 16 Jun 2020 09:15:27: 16000000 INFO @ Tue, 16 Jun 2020 09:15:31: 21000000 INFO @ Tue, 16 Jun 2020 09:15:34: 26000000 INFO @ Tue, 16 Jun 2020 09:15:34: 17000000 INFO @ Tue, 16 Jun 2020 09:15:39: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:15:41: 27000000 INFO @ Tue, 16 Jun 2020 09:15:42: 18000000 INFO @ Tue, 16 Jun 2020 09:15:47: 23000000 INFO @ Tue, 16 Jun 2020 09:15:49: 28000000 INFO @ Tue, 16 Jun 2020 09:15:50: 19000000 INFO @ Tue, 16 Jun 2020 09:15:54: 24000000 INFO @ Tue, 16 Jun 2020 09:15:57: 29000000 INFO @ Tue, 16 Jun 2020 09:15:58: 20000000 INFO @ Tue, 16 Jun 2020 09:16:02: 25000000 INFO @ Tue, 16 Jun 2020 09:16:02: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:16:02: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:16:02: #1 total tags in treatment: 13019332 INFO @ Tue, 16 Jun 2020 09:16:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:16:02: #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 09:16:02: #1 tags after filtering in treatment: 11296288 INFO @ Tue, 16 Jun 2020 09:16:02: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 16 Jun 2020 09:16:02: #1 finished! INFO @ Tue, 16 Jun 2020 09:16:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:16:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:16:03: #2 number of paired peaks: 184 WARNING @ Tue, 16 Jun 2020 09:16:03: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Tue, 16 Jun 2020 09:16:03: start model_add_line... INFO @ Tue, 16 Jun 2020 09:16:03: start X-correlation... INFO @ Tue, 16 Jun 2020 09:16:03: end of X-cor INFO @ Tue, 16 Jun 2020 09:16:03: #2 finished! INFO @ Tue, 16 Jun 2020 09:16:03: #2 predicted fragment length is 95 bps INFO @ Tue, 16 Jun 2020 09:16:03: #2 alternative fragment length(s) may be 4,95 bps INFO @ Tue, 16 Jun 2020 09:16:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085370/SRX4085370.05_model.r WARNING @ Tue, 16 Jun 2020 09:16:03: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:16:03: #2 You may need to consider one of the other alternative d(s): 4,95 WARNING @ Tue, 16 Jun 2020 09:16:03: #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 09:16:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:16:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:16:05: 21000000 INFO @ Tue, 16 Jun 2020 09:16:09: 26000000 INFO @ Tue, 16 Jun 2020 09:16:13: 22000000 INFO @ Tue, 16 Jun 2020 09:16:17: 27000000 INFO @ Tue, 16 Jun 2020 09:16:21: 23000000 INFO @ Tue, 16 Jun 2020 09:16:24: 28000000 INFO @ Tue, 16 Jun 2020 09:16:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:16:28: 24000000 INFO @ Tue, 16 Jun 2020 09:16:32: 29000000 INFO @ Tue, 16 Jun 2020 09:16:35: 25000000 INFO @ Tue, 16 Jun 2020 09:16:37: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:16:37: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:16:37: #1 total tags in treatment: 13019332 INFO @ Tue, 16 Jun 2020 09:16:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:16:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:16:37: #1 tags after filtering in treatment: 11296288 INFO @ Tue, 16 Jun 2020 09:16:37: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 16 Jun 2020 09:16:37: #1 finished! INFO @ Tue, 16 Jun 2020 09:16:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:16:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:16:38: #2 number of paired peaks: 184 WARNING @ Tue, 16 Jun 2020 09:16:38: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Tue, 16 Jun 2020 09:16:38: start model_add_line... INFO @ Tue, 16 Jun 2020 09:16:38: start X-correlation... INFO @ Tue, 16 Jun 2020 09:16:38: end of X-cor INFO @ Tue, 16 Jun 2020 09:16:38: #2 finished! INFO @ Tue, 16 Jun 2020 09:16:38: #2 predicted fragment length is 95 bps INFO @ Tue, 16 Jun 2020 09:16:38: #2 alternative fragment length(s) may be 4,95 bps INFO @ Tue, 16 Jun 2020 09:16:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085370/SRX4085370.10_model.r WARNING @ Tue, 16 Jun 2020 09:16:38: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:16:38: #2 You may need to consider one of the other alternative d(s): 4,95 WARNING @ Tue, 16 Jun 2020 09:16:38: #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 09:16:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:16:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:16:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085370/SRX4085370.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:16:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085370/SRX4085370.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:16:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085370/SRX4085370.05_summits.bed INFO @ Tue, 16 Jun 2020 09:16:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4071 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:16:42: 26000000 INFO @ Tue, 16 Jun 2020 09:16:49: 27000000 INFO @ Tue, 16 Jun 2020 09:16:55: 28000000 INFO @ Tue, 16 Jun 2020 09:17:02: 29000000 INFO @ Tue, 16 Jun 2020 09:17:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:17:06: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:17:06: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:17:06: #1 total tags in treatment: 13019332 INFO @ Tue, 16 Jun 2020 09:17:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:17:06: #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 09:17:07: #1 tags after filtering in treatment: 11296288 INFO @ Tue, 16 Jun 2020 09:17:07: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 16 Jun 2020 09:17:07: #1 finished! INFO @ Tue, 16 Jun 2020 09:17:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:17:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:17:08: #2 number of paired peaks: 184 WARNING @ Tue, 16 Jun 2020 09:17:08: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Tue, 16 Jun 2020 09:17:08: start model_add_line... INFO @ Tue, 16 Jun 2020 09:17:08: start X-correlation... INFO @ Tue, 16 Jun 2020 09:17:08: end of X-cor INFO @ Tue, 16 Jun 2020 09:17:08: #2 finished! INFO @ Tue, 16 Jun 2020 09:17:08: #2 predicted fragment length is 95 bps INFO @ Tue, 16 Jun 2020 09:17:08: #2 alternative fragment length(s) may be 4,95 bps INFO @ Tue, 16 Jun 2020 09:17:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085370/SRX4085370.20_model.r WARNING @ Tue, 16 Jun 2020 09:17:08: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:17:08: #2 You may need to consider one of the other alternative d(s): 4,95 WARNING @ Tue, 16 Jun 2020 09:17:08: #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 09:17:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:17:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:17:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085370/SRX4085370.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:17:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085370/SRX4085370.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:17:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085370/SRX4085370.10_summits.bed INFO @ Tue, 16 Jun 2020 09:17:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1859 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:17:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:17:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085370/SRX4085370.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:17:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085370/SRX4085370.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:17:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085370/SRX4085370.20_summits.bed INFO @ Tue, 16 Jun 2020 09:17:44: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (414 records, 4 fields): 2 millis CompletedMACS2peakCalling