Job ID = 6368862 SRX = SRX6619560 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-16T00:27:49 prefetch.2.10.7: 1) Downloading 'SRR9866049'... 2020-06-16T00:27:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:40:19 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:40:19 prefetch.2.10.7: 1) 'SRR9866049' was downloaded successfully 2020-06-16T00:40:19 prefetch.2.10.7: 'SRR9866049' has 0 unresolved dependencies Read 35821108 spots for SRR9866049/SRR9866049.sra Written 35821108 spots for SRR9866049/SRR9866049.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: 00:49:00 35821108 reads; of these: 35821108 (100.00%) were paired; of these: 21558950 (60.19%) aligned concordantly 0 times 11912825 (33.26%) aligned concordantly exactly 1 time 2349333 (6.56%) aligned concordantly >1 times ---- 21558950 pairs aligned concordantly 0 times; of these: 4707279 (21.83%) aligned discordantly 1 time ---- 16851671 pairs aligned 0 times concordantly or discordantly; of these: 33703342 mates make up the pairs; of these: 31669171 (93.96%) aligned 0 times 711810 (2.11%) aligned exactly 1 time 1322361 (3.92%) aligned >1 times 55.80% overall alignment rate Time searching: 00:49:00 Overall time: 00:49:00 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] 2579972 / 18810307 = 0.1372 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 10:49:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6619560/SRX6619560.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6619560/SRX6619560.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6619560/SRX6619560.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6619560/SRX6619560.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 10:49:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:49:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:49:07: 1000000 INFO @ Tue, 16 Jun 2020 10:49:14: 2000000 INFO @ Tue, 16 Jun 2020 10:49:21: 3000000 INFO @ Tue, 16 Jun 2020 10:49:28: 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 10:49:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6619560/SRX6619560.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6619560/SRX6619560.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6619560/SRX6619560.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6619560/SRX6619560.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 10:49:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:49:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:49:35: 5000000 INFO @ Tue, 16 Jun 2020 10:49:38: 1000000 INFO @ Tue, 16 Jun 2020 10:49:43: 6000000 INFO @ Tue, 16 Jun 2020 10:49:45: 2000000 INFO @ Tue, 16 Jun 2020 10:49:50: 7000000 INFO @ Tue, 16 Jun 2020 10:49:53: 3000000 INFO @ Tue, 16 Jun 2020 10:49:58: 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 10:50:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6619560/SRX6619560.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6619560/SRX6619560.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6619560/SRX6619560.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6619560/SRX6619560.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 10:50:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:50:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:50:00: 4000000 INFO @ Tue, 16 Jun 2020 10:50:05: 9000000 INFO @ Tue, 16 Jun 2020 10:50:08: 5000000 INFO @ Tue, 16 Jun 2020 10:50:08: 1000000 INFO @ Tue, 16 Jun 2020 10:50:13: 10000000 INFO @ Tue, 16 Jun 2020 10:50:16: 6000000 INFO @ Tue, 16 Jun 2020 10:50:16: 2000000 INFO @ Tue, 16 Jun 2020 10:50:21: 11000000 INFO @ Tue, 16 Jun 2020 10:50:24: 7000000 INFO @ Tue, 16 Jun 2020 10:50:24: 3000000 INFO @ Tue, 16 Jun 2020 10:50:29: 12000000 INFO @ Tue, 16 Jun 2020 10:50:32: 4000000 INFO @ Tue, 16 Jun 2020 10:50:32: 8000000 INFO @ Tue, 16 Jun 2020 10:50:37: 13000000 INFO @ Tue, 16 Jun 2020 10:50:40: 5000000 INFO @ Tue, 16 Jun 2020 10:50:40: 9000000 INFO @ Tue, 16 Jun 2020 10:50:45: 14000000 INFO @ Tue, 16 Jun 2020 10:50:48: 6000000 INFO @ Tue, 16 Jun 2020 10:50:48: 10000000 INFO @ Tue, 16 Jun 2020 10:50:53: 15000000 INFO @ Tue, 16 Jun 2020 10:50:56: 7000000 INFO @ Tue, 16 Jun 2020 10:50:56: 11000000 INFO @ Tue, 16 Jun 2020 10:51:01: 16000000 INFO @ Tue, 16 Jun 2020 10:51:03: 8000000 INFO @ Tue, 16 Jun 2020 10:51:04: 12000000 INFO @ Tue, 16 Jun 2020 10:51:08: 17000000 INFO @ Tue, 16 Jun 2020 10:51:11: 9000000 INFO @ Tue, 16 Jun 2020 10:51:12: 13000000 INFO @ Tue, 16 Jun 2020 10:51:16: 18000000 INFO @ Tue, 16 Jun 2020 10:51:19: 10000000 INFO @ Tue, 16 Jun 2020 10:51:20: 14000000 INFO @ Tue, 16 Jun 2020 10:51:24: 19000000 INFO @ Tue, 16 Jun 2020 10:51:26: 11000000 INFO @ Tue, 16 Jun 2020 10:51:28: 15000000 INFO @ Tue, 16 Jun 2020 10:51:32: 20000000 INFO @ Tue, 16 Jun 2020 10:51:34: 12000000 INFO @ Tue, 16 Jun 2020 10:51:36: 16000000 INFO @ Tue, 16 Jun 2020 10:51:39: 21000000 INFO @ Tue, 16 Jun 2020 10:51:42: 13000000 INFO @ Tue, 16 Jun 2020 10:51:43: 17000000 INFO @ Tue, 16 Jun 2020 10:51:47: 22000000 INFO @ Tue, 16 Jun 2020 10:51:49: 14000000 INFO @ Tue, 16 Jun 2020 10:51:51: 18000000 INFO @ Tue, 16 Jun 2020 10:51:55: 23000000 INFO @ Tue, 16 Jun 2020 10:51:57: 15000000 INFO @ Tue, 16 Jun 2020 10:51:59: 19000000 INFO @ Tue, 16 Jun 2020 10:52:02: 24000000 INFO @ Tue, 16 Jun 2020 10:52:05: 16000000 INFO @ Tue, 16 Jun 2020 10:52:07: 20000000 INFO @ Tue, 16 Jun 2020 10:52:10: 25000000 INFO @ Tue, 16 Jun 2020 10:52:12: 17000000 INFO @ Tue, 16 Jun 2020 10:52:14: 21000000 INFO @ Tue, 16 Jun 2020 10:52:18: 26000000 INFO @ Tue, 16 Jun 2020 10:52:20: 18000000 INFO @ Tue, 16 Jun 2020 10:52:22: 22000000 INFO @ Tue, 16 Jun 2020 10:52:25: 27000000 INFO @ Tue, 16 Jun 2020 10:52:28: 19000000 INFO @ Tue, 16 Jun 2020 10:52:30: 23000000 INFO @ Tue, 16 Jun 2020 10:52:33: 28000000 INFO @ Tue, 16 Jun 2020 10:52:35: 20000000 INFO @ Tue, 16 Jun 2020 10:52:38: 24000000 INFO @ Tue, 16 Jun 2020 10:52:41: 29000000 INFO @ Tue, 16 Jun 2020 10:52:43: 21000000 INFO @ Tue, 16 Jun 2020 10:52:45: 25000000 INFO @ Tue, 16 Jun 2020 10:52:49: 30000000 INFO @ Tue, 16 Jun 2020 10:52:51: 22000000 INFO @ Tue, 16 Jun 2020 10:52:53: 26000000 INFO @ Tue, 16 Jun 2020 10:52:57: 31000000 INFO @ Tue, 16 Jun 2020 10:52:59: 23000000 INFO @ Tue, 16 Jun 2020 10:53:01: 27000000 INFO @ Tue, 16 Jun 2020 10:53:04: 32000000 INFO @ Tue, 16 Jun 2020 10:53:07: 24000000 INFO @ Tue, 16 Jun 2020 10:53:09: 28000000 INFO @ Tue, 16 Jun 2020 10:53:12: 33000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:53:15: 25000000 INFO @ Tue, 16 Jun 2020 10:53:17: 29000000 INFO @ Tue, 16 Jun 2020 10:53:20: 34000000 INFO @ Tue, 16 Jun 2020 10:53:23: 26000000 INFO @ Tue, 16 Jun 2020 10:53:25: 30000000 INFO @ Tue, 16 Jun 2020 10:53:27: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 10:53:27: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 10:53:27: #1 total tags in treatment: 12244018 INFO @ Tue, 16 Jun 2020 10:53:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:53:27: #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 10:53:27: #1 tags after filtering in treatment: 10754651 INFO @ Tue, 16 Jun 2020 10:53:27: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 16 Jun 2020 10:53:27: #1 finished! INFO @ Tue, 16 Jun 2020 10:53:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:53:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:53:28: #2 number of paired peaks: 375 WARNING @ Tue, 16 Jun 2020 10:53:28: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Tue, 16 Jun 2020 10:53:28: start model_add_line... INFO @ Tue, 16 Jun 2020 10:53:28: start X-correlation... INFO @ Tue, 16 Jun 2020 10:53:28: end of X-cor INFO @ Tue, 16 Jun 2020 10:53:28: #2 finished! INFO @ Tue, 16 Jun 2020 10:53:28: #2 predicted fragment length is 214 bps INFO @ Tue, 16 Jun 2020 10:53:28: #2 alternative fragment length(s) may be 214 bps INFO @ Tue, 16 Jun 2020 10:53:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6619560/SRX6619560.05_model.r WARNING @ Tue, 16 Jun 2020 10:53:28: #2 Since the d (214) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:53:28: #2 You may need to consider one of the other alternative d(s): 214 WARNING @ Tue, 16 Jun 2020 10:53:28: #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 10:53:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:53:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:53:32: 27000000 INFO @ Tue, 16 Jun 2020 10:53:33: 31000000 INFO @ Tue, 16 Jun 2020 10:53:40: 28000000 INFO @ Tue, 16 Jun 2020 10:53:41: 32000000 INFO @ Tue, 16 Jun 2020 10:53:49: 29000000 INFO @ Tue, 16 Jun 2020 10:53:49: 33000000 INFO @ Tue, 16 Jun 2020 10:53:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:53:57: 34000000 INFO @ Tue, 16 Jun 2020 10:53:57: 30000000 INFO @ Tue, 16 Jun 2020 10:54:04: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 10:54:04: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 10:54:04: #1 total tags in treatment: 12244018 INFO @ Tue, 16 Jun 2020 10:54:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:54:04: #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 10:54:04: #1 tags after filtering in treatment: 10754651 INFO @ Tue, 16 Jun 2020 10:54:04: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 16 Jun 2020 10:54:04: #1 finished! INFO @ Tue, 16 Jun 2020 10:54:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:54:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:54:05: #2 number of paired peaks: 375 WARNING @ Tue, 16 Jun 2020 10:54:05: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Tue, 16 Jun 2020 10:54:05: start model_add_line... INFO @ Tue, 16 Jun 2020 10:54:05: start X-correlation... INFO @ Tue, 16 Jun 2020 10:54:05: end of X-cor INFO @ Tue, 16 Jun 2020 10:54:05: #2 finished! INFO @ Tue, 16 Jun 2020 10:54:05: #2 predicted fragment length is 214 bps INFO @ Tue, 16 Jun 2020 10:54:05: #2 alternative fragment length(s) may be 214 bps INFO @ Tue, 16 Jun 2020 10:54:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6619560/SRX6619560.10_model.r WARNING @ Tue, 16 Jun 2020 10:54:05: #2 Since the d (214) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:54:05: #2 You may need to consider one of the other alternative d(s): 214 WARNING @ Tue, 16 Jun 2020 10:54:05: #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 10:54:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:54:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:54:05: 31000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:54:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6619560/SRX6619560.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:54:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6619560/SRX6619560.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:54:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6619560/SRX6619560.05_summits.bed INFO @ Tue, 16 Jun 2020 10:54:09: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (17595 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:54:13: 32000000 INFO @ Tue, 16 Jun 2020 10:54:21: 33000000 INFO @ Tue, 16 Jun 2020 10:54:28: 34000000 INFO @ Tue, 16 Jun 2020 10:54:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:54:35: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 10:54:35: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 10:54:35: #1 total tags in treatment: 12244018 INFO @ Tue, 16 Jun 2020 10:54:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:54:35: #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 10:54:35: #1 tags after filtering in treatment: 10754651 INFO @ Tue, 16 Jun 2020 10:54:35: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 16 Jun 2020 10:54:35: #1 finished! INFO @ Tue, 16 Jun 2020 10:54:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:54:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:54:36: #2 number of paired peaks: 375 WARNING @ Tue, 16 Jun 2020 10:54:36: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Tue, 16 Jun 2020 10:54:36: start model_add_line... INFO @ Tue, 16 Jun 2020 10:54:36: start X-correlation... INFO @ Tue, 16 Jun 2020 10:54:36: end of X-cor INFO @ Tue, 16 Jun 2020 10:54:36: #2 finished! INFO @ Tue, 16 Jun 2020 10:54:36: #2 predicted fragment length is 214 bps INFO @ Tue, 16 Jun 2020 10:54:36: #2 alternative fragment length(s) may be 214 bps INFO @ Tue, 16 Jun 2020 10:54:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6619560/SRX6619560.20_model.r WARNING @ Tue, 16 Jun 2020 10:54:36: #2 Since the d (214) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:54:36: #2 You may need to consider one of the other alternative d(s): 214 WARNING @ Tue, 16 Jun 2020 10:54:36: #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 10:54:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:54:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:54:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6619560/SRX6619560.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:54:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6619560/SRX6619560.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:54:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6619560/SRX6619560.10_summits.bed INFO @ Tue, 16 Jun 2020 10:54:46: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4991 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:55:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:55:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6619560/SRX6619560.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:55:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6619560/SRX6619560.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:55:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6619560/SRX6619560.20_summits.bed INFO @ Tue, 16 Jun 2020 10:55:17: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (375 records, 4 fields): 1 millis CompletedMACS2peakCalling