Job ID = 6368837 SRX = SRX6619536 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-16T00:27:35 prefetch.2.10.7: 1) Downloading 'SRR9866072'... 2020-06-16T00:27:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:44:42 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:44:42 prefetch.2.10.7: 1) 'SRR9866072' was downloaded successfully 2020-06-16T00:44:42 prefetch.2.10.7: 'SRR9866072' has 0 unresolved dependencies Read 32260840 spots for SRR9866072/SRR9866072.sra Written 32260840 spots for SRR9866072/SRR9866072.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: 01:00:00 32260840 reads; of these: 32260840 (100.00%) were paired; of these: 19673009 (60.98%) aligned concordantly 0 times 9131564 (28.31%) aligned concordantly exactly 1 time 3456267 (10.71%) aligned concordantly >1 times ---- 19673009 pairs aligned concordantly 0 times; of these: 7141734 (36.30%) aligned discordantly 1 time ---- 12531275 pairs aligned 0 times concordantly or discordantly; of these: 25062550 mates make up the pairs; of these: 21284913 (84.93%) aligned 0 times 1085123 (4.33%) aligned exactly 1 time 2692514 (10.74%) aligned >1 times 67.01% overall alignment rate Time searching: 01:00:00 Overall time: 01:00:00 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 32 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] 3343343 / 19402756 = 0.1723 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 11:08:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6619536/SRX6619536.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6619536/SRX6619536.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6619536/SRX6619536.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6619536/SRX6619536.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 11:08:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 11:08:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 11:08:19: 1000000 INFO @ Tue, 16 Jun 2020 11:08:31: 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 11:08:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6619536/SRX6619536.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6619536/SRX6619536.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6619536/SRX6619536.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6619536/SRX6619536.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 11:08:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 11:08:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 11:08:43: 3000000 INFO @ Tue, 16 Jun 2020 11:08:52: 1000000 INFO @ Tue, 16 Jun 2020 11:08:56: 4000000 INFO @ Tue, 16 Jun 2020 11:09:06: 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 11:09:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6619536/SRX6619536.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6619536/SRX6619536.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6619536/SRX6619536.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6619536/SRX6619536.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 11:09:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 11:09:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 11:09:10: 5000000 INFO @ Tue, 16 Jun 2020 11:09:20: 3000000 INFO @ Tue, 16 Jun 2020 11:09:23: 1000000 INFO @ Tue, 16 Jun 2020 11:09:24: 6000000 INFO @ Tue, 16 Jun 2020 11:09:34: 4000000 INFO @ Tue, 16 Jun 2020 11:09:38: 7000000 INFO @ Tue, 16 Jun 2020 11:09:38: 2000000 INFO @ Tue, 16 Jun 2020 11:09:49: 5000000 INFO @ Tue, 16 Jun 2020 11:09:53: 8000000 INFO @ Tue, 16 Jun 2020 11:09:53: 3000000 INFO @ Tue, 16 Jun 2020 11:10:04: 6000000 INFO @ Tue, 16 Jun 2020 11:10:07: 4000000 INFO @ Tue, 16 Jun 2020 11:10:08: 9000000 INFO @ Tue, 16 Jun 2020 11:10:19: 7000000 INFO @ Tue, 16 Jun 2020 11:10:21: 5000000 INFO @ Tue, 16 Jun 2020 11:10:23: 10000000 INFO @ Tue, 16 Jun 2020 11:10:34: 8000000 INFO @ Tue, 16 Jun 2020 11:10:34: 6000000 INFO @ Tue, 16 Jun 2020 11:10:38: 11000000 INFO @ Tue, 16 Jun 2020 11:10:48: 7000000 INFO @ Tue, 16 Jun 2020 11:10:48: 9000000 INFO @ Tue, 16 Jun 2020 11:10:53: 12000000 INFO @ Tue, 16 Jun 2020 11:11:02: 10000000 INFO @ Tue, 16 Jun 2020 11:11:02: 8000000 INFO @ Tue, 16 Jun 2020 11:11:08: 13000000 INFO @ Tue, 16 Jun 2020 11:11:16: 11000000 INFO @ Tue, 16 Jun 2020 11:11:17: 9000000 INFO @ Tue, 16 Jun 2020 11:11:22: 14000000 INFO @ Tue, 16 Jun 2020 11:11:29: 12000000 INFO @ Tue, 16 Jun 2020 11:11:32: 10000000 INFO @ Tue, 16 Jun 2020 11:11:36: 15000000 INFO @ Tue, 16 Jun 2020 11:11:42: 13000000 INFO @ Tue, 16 Jun 2020 11:11:48: 11000000 INFO @ Tue, 16 Jun 2020 11:11:51: 16000000 INFO @ Tue, 16 Jun 2020 11:11:55: 14000000 INFO @ Tue, 16 Jun 2020 11:12:02: 12000000 INFO @ Tue, 16 Jun 2020 11:12:04: 17000000 INFO @ Tue, 16 Jun 2020 11:12:08: 15000000 INFO @ Tue, 16 Jun 2020 11:12:16: 13000000 INFO @ Tue, 16 Jun 2020 11:12:18: 18000000 INFO @ Tue, 16 Jun 2020 11:12:21: 16000000 INFO @ Tue, 16 Jun 2020 11:12:30: 14000000 INFO @ Tue, 16 Jun 2020 11:12:32: 19000000 INFO @ Tue, 16 Jun 2020 11:12:34: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 11:12:43: 15000000 INFO @ Tue, 16 Jun 2020 11:12:46: 20000000 INFO @ Tue, 16 Jun 2020 11:12:47: 18000000 INFO @ Tue, 16 Jun 2020 11:12:57: 16000000 INFO @ Tue, 16 Jun 2020 11:13:00: 21000000 INFO @ Tue, 16 Jun 2020 11:13:01: 19000000 INFO @ Tue, 16 Jun 2020 11:13:11: 17000000 INFO @ Tue, 16 Jun 2020 11:13:13: 22000000 INFO @ Tue, 16 Jun 2020 11:13:14: 20000000 INFO @ Tue, 16 Jun 2020 11:13:25: 18000000 INFO @ Tue, 16 Jun 2020 11:13:27: 23000000 INFO @ Tue, 16 Jun 2020 11:13:27: 21000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 11:13:39: 19000000 INFO @ Tue, 16 Jun 2020 11:13:41: 22000000 INFO @ Tue, 16 Jun 2020 11:13:41: 24000000 INFO @ Tue, 16 Jun 2020 11:13:53: 20000000 INFO @ Tue, 16 Jun 2020 11:13:54: 23000000 INFO @ Tue, 16 Jun 2020 11:13:54: 25000000 INFO @ Tue, 16 Jun 2020 11:14:07: 21000000 INFO @ Tue, 16 Jun 2020 11:14:07: 24000000 INFO @ Tue, 16 Jun 2020 11:14:07: 26000000 INFO @ Tue, 16 Jun 2020 11:14:20: 22000000 INFO @ Tue, 16 Jun 2020 11:14:21: 25000000 INFO @ Tue, 16 Jun 2020 11:14:21: 27000000 INFO @ Tue, 16 Jun 2020 11:14:34: 23000000 INFO @ Tue, 16 Jun 2020 11:14:34: 26000000 INFO @ Tue, 16 Jun 2020 11:14:35: 28000000 INFO @ Tue, 16 Jun 2020 11:14:47: 27000000 INFO @ Tue, 16 Jun 2020 11:14:47: 24000000 INFO @ Tue, 16 Jun 2020 11:14:49: 29000000 INFO @ Tue, 16 Jun 2020 11:15:00: 28000000 INFO @ Tue, 16 Jun 2020 11:15:01: 25000000 INFO @ Tue, 16 Jun 2020 11:15:02: 30000000 INFO @ Tue, 16 Jun 2020 11:15:14: 29000000 INFO @ Tue, 16 Jun 2020 11:15:14: 26000000 INFO @ Tue, 16 Jun 2020 11:15:16: 31000000 INFO @ Tue, 16 Jun 2020 11:15:28: 27000000 INFO @ Tue, 16 Jun 2020 11:15:28: 30000000 INFO @ Tue, 16 Jun 2020 11:15:30: 32000000 INFO @ Tue, 16 Jun 2020 11:15:42: 28000000 INFO @ Tue, 16 Jun 2020 11:15:43: 31000000 INFO @ Tue, 16 Jun 2020 11:15:44: 33000000 INFO @ Tue, 16 Jun 2020 11:15:55: 29000000 INFO @ Tue, 16 Jun 2020 11:15:57: 32000000 INFO @ Tue, 16 Jun 2020 11:15:58: 34000000 INFO @ Tue, 16 Jun 2020 11:16:09: 30000000 INFO @ Tue, 16 Jun 2020 11:16:11: 35000000 INFO @ Tue, 16 Jun 2020 11:16:11: 33000000 INFO @ Tue, 16 Jun 2020 11:16:23: 31000000 INFO @ Tue, 16 Jun 2020 11:16:25: 34000000 INFO @ Tue, 16 Jun 2020 11:16:25: 36000000 INFO @ Tue, 16 Jun 2020 11:16:33: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 11:16:33: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 11:16:33: #1 total tags in treatment: 10177062 INFO @ Tue, 16 Jun 2020 11:16:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 11:16:33: #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 11:16:33: #1 tags after filtering in treatment: 7984844 INFO @ Tue, 16 Jun 2020 11:16:33: #1 Redundant rate of treatment: 0.22 INFO @ Tue, 16 Jun 2020 11:16:33: #1 finished! INFO @ Tue, 16 Jun 2020 11:16:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 11:16:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 11:16:33: #2 number of paired peaks: 572 WARNING @ Tue, 16 Jun 2020 11:16:33: Fewer paired peaks (572) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 572 pairs to build model! INFO @ Tue, 16 Jun 2020 11:16:33: start model_add_line... INFO @ Tue, 16 Jun 2020 11:16:33: start X-correlation... INFO @ Tue, 16 Jun 2020 11:16:33: end of X-cor INFO @ Tue, 16 Jun 2020 11:16:33: #2 finished! INFO @ Tue, 16 Jun 2020 11:16:33: #2 predicted fragment length is 221 bps INFO @ Tue, 16 Jun 2020 11:16:33: #2 alternative fragment length(s) may be 221 bps INFO @ Tue, 16 Jun 2020 11:16:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6619536/SRX6619536.05_model.r WARNING @ Tue, 16 Jun 2020 11:16:33: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 11:16:33: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Tue, 16 Jun 2020 11:16:33: #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 11:16:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 11:16:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 11:16:37: 32000000 INFO @ Tue, 16 Jun 2020 11:16:38: 35000000 INFO @ Tue, 16 Jun 2020 11:16:50: 33000000 INFO @ Tue, 16 Jun 2020 11:16:51: 36000000 INFO @ Tue, 16 Jun 2020 11:16:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 11:16:59: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 11:16:59: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 11:16:59: #1 total tags in treatment: 10177062 INFO @ Tue, 16 Jun 2020 11:16:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 11:16:59: #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 11:16:59: #1 tags after filtering in treatment: 7984844 INFO @ Tue, 16 Jun 2020 11:16:59: #1 Redundant rate of treatment: 0.22 INFO @ Tue, 16 Jun 2020 11:16:59: #1 finished! INFO @ Tue, 16 Jun 2020 11:16:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 11:16:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 11:16:59: #2 number of paired peaks: 572 WARNING @ Tue, 16 Jun 2020 11:16:59: Fewer paired peaks (572) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 572 pairs to build model! INFO @ Tue, 16 Jun 2020 11:16:59: start model_add_line... INFO @ Tue, 16 Jun 2020 11:16:59: start X-correlation... INFO @ Tue, 16 Jun 2020 11:16:59: end of X-cor INFO @ Tue, 16 Jun 2020 11:16:59: #2 finished! INFO @ Tue, 16 Jun 2020 11:16:59: #2 predicted fragment length is 221 bps INFO @ Tue, 16 Jun 2020 11:16:59: #2 alternative fragment length(s) may be 221 bps INFO @ Tue, 16 Jun 2020 11:16:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6619536/SRX6619536.10_model.r WARNING @ Tue, 16 Jun 2020 11:16:59: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 11:16:59: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Tue, 16 Jun 2020 11:16:59: #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 11:16:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 11:16:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 11:17:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6619536/SRX6619536.05_peaks.xls INFO @ Tue, 16 Jun 2020 11:17:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6619536/SRX6619536.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 11:17:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6619536/SRX6619536.05_summits.bed INFO @ Tue, 16 Jun 2020 11:17:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (807 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 11:17:02: 34000000 INFO @ Tue, 16 Jun 2020 11:17:14: 35000000 INFO @ Tue, 16 Jun 2020 11:17:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 11:17:26: 36000000 INFO @ Tue, 16 Jun 2020 11:17:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6619536/SRX6619536.10_peaks.xls INFO @ Tue, 16 Jun 2020 11:17:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6619536/SRX6619536.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 11:17:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6619536/SRX6619536.10_summits.bed INFO @ Tue, 16 Jun 2020 11:17:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (382 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 11:17:32: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 11:17:32: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 11:17:32: #1 total tags in treatment: 10177062 INFO @ Tue, 16 Jun 2020 11:17:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 11:17:32: #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 11:17:32: #1 tags after filtering in treatment: 7984844 INFO @ Tue, 16 Jun 2020 11:17:32: #1 Redundant rate of treatment: 0.22 INFO @ Tue, 16 Jun 2020 11:17:32: #1 finished! INFO @ Tue, 16 Jun 2020 11:17:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 11:17:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 11:17:33: #2 number of paired peaks: 572 WARNING @ Tue, 16 Jun 2020 11:17:33: Fewer paired peaks (572) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 572 pairs to build model! INFO @ Tue, 16 Jun 2020 11:17:33: start model_add_line... INFO @ Tue, 16 Jun 2020 11:17:33: start X-correlation... INFO @ Tue, 16 Jun 2020 11:17:33: end of X-cor INFO @ Tue, 16 Jun 2020 11:17:33: #2 finished! INFO @ Tue, 16 Jun 2020 11:17:33: #2 predicted fragment length is 221 bps INFO @ Tue, 16 Jun 2020 11:17:33: #2 alternative fragment length(s) may be 221 bps INFO @ Tue, 16 Jun 2020 11:17:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6619536/SRX6619536.20_model.r WARNING @ Tue, 16 Jun 2020 11:17:33: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 11:17:33: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Tue, 16 Jun 2020 11:17:33: #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 11:17:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 11:17:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 11:17:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 11:18:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6619536/SRX6619536.20_peaks.xls INFO @ Tue, 16 Jun 2020 11:18:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6619536/SRX6619536.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 11:18:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6619536/SRX6619536.20_summits.bed INFO @ Tue, 16 Jun 2020 11:18:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (195 records, 4 fields): 1 millis CompletedMACS2peakCalling