Job ID = 6365821 SRX = ERX1485062 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T22:27:14 prefetch.2.10.7: 1) Downloading 'ERR1414279'... 2020-06-15T22:27:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:40:22 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:40:22 prefetch.2.10.7: 1) 'ERR1414279' was downloaded successfully Read 30362235 spots for ERR1414279/ERR1414279.sra Written 30362235 spots for ERR1414279/ERR1414279.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: 00:44:34 30362235 reads; of these: 30362235 (100.00%) were paired; of these: 385952 (1.27%) aligned concordantly 0 times 26442141 (87.09%) aligned concordantly exactly 1 time 3534142 (11.64%) aligned concordantly >1 times ---- 385952 pairs aligned concordantly 0 times; of these: 15683 (4.06%) aligned discordantly 1 time ---- 370269 pairs aligned 0 times concordantly or discordantly; of these: 740538 mates make up the pairs; of these: 436753 (58.98%) aligned 0 times 231553 (31.27%) aligned exactly 1 time 72232 (9.75%) aligned >1 times 99.28% overall alignment rate Time searching: 00:44:34 Overall time: 00:44:34 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 28 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] 13397694 / 29981559 = 0.4469 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 08:50:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/ERX1485062/ERX1485062.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/ERX1485062/ERX1485062.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/ERX1485062/ERX1485062.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/ERX1485062/ERX1485062.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 08:50:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:50:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:50:45: 1000000 INFO @ Tue, 16 Jun 2020 08:50:52: 2000000 INFO @ Tue, 16 Jun 2020 08:51:00: 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 08:51:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/ERX1485062/ERX1485062.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/ERX1485062/ERX1485062.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/ERX1485062/ERX1485062.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/ERX1485062/ERX1485062.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 08:51:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:51:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:51:08: 4000000 INFO @ Tue, 16 Jun 2020 08:51:15: 1000000 INFO @ Tue, 16 Jun 2020 08:51:16: 5000000 INFO @ Tue, 16 Jun 2020 08:51:22: 2000000 INFO @ Tue, 16 Jun 2020 08:51:24: 6000000 INFO @ Tue, 16 Jun 2020 08:51:30: 3000000 INFO @ Tue, 16 Jun 2020 08:51:33: 7000000 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 08:51:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/ERX1485062/ERX1485062.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/ERX1485062/ERX1485062.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/ERX1485062/ERX1485062.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/ERX1485062/ERX1485062.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 08:51:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:51:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:51:38: 4000000 INFO @ Tue, 16 Jun 2020 08:51:41: 8000000 INFO @ Tue, 16 Jun 2020 08:51:45: 1000000 INFO @ Tue, 16 Jun 2020 08:51:46: 5000000 INFO @ Tue, 16 Jun 2020 08:51:50: 9000000 INFO @ Tue, 16 Jun 2020 08:51:53: 2000000 INFO @ Tue, 16 Jun 2020 08:51:54: 6000000 INFO @ Tue, 16 Jun 2020 08:51:58: 10000000 INFO @ Tue, 16 Jun 2020 08:52:01: 3000000 INFO @ Tue, 16 Jun 2020 08:52:02: 7000000 INFO @ Tue, 16 Jun 2020 08:52:07: 11000000 INFO @ Tue, 16 Jun 2020 08:52:09: 4000000 INFO @ Tue, 16 Jun 2020 08:52:10: 8000000 INFO @ Tue, 16 Jun 2020 08:52:16: 12000000 INFO @ Tue, 16 Jun 2020 08:52:17: 5000000 INFO @ Tue, 16 Jun 2020 08:52:18: 9000000 INFO @ Tue, 16 Jun 2020 08:52:25: 13000000 INFO @ Tue, 16 Jun 2020 08:52:25: 6000000 INFO @ Tue, 16 Jun 2020 08:52:26: 10000000 INFO @ Tue, 16 Jun 2020 08:52:33: 14000000 INFO @ Tue, 16 Jun 2020 08:52:33: 7000000 INFO @ Tue, 16 Jun 2020 08:52:35: 11000000 INFO @ Tue, 16 Jun 2020 08:52:41: 8000000 INFO @ Tue, 16 Jun 2020 08:52:42: 15000000 INFO @ Tue, 16 Jun 2020 08:52:43: 12000000 INFO @ Tue, 16 Jun 2020 08:52:49: 9000000 INFO @ Tue, 16 Jun 2020 08:52:50: 16000000 INFO @ Tue, 16 Jun 2020 08:52:51: 13000000 INFO @ Tue, 16 Jun 2020 08:52:57: 10000000 INFO @ Tue, 16 Jun 2020 08:52:59: 14000000 INFO @ Tue, 16 Jun 2020 08:52:59: 17000000 INFO @ Tue, 16 Jun 2020 08:53:06: 11000000 INFO @ Tue, 16 Jun 2020 08:53:07: 15000000 INFO @ Tue, 16 Jun 2020 08:53:07: 18000000 INFO @ Tue, 16 Jun 2020 08:53:14: 12000000 INFO @ Tue, 16 Jun 2020 08:53:15: 16000000 INFO @ Tue, 16 Jun 2020 08:53:16: 19000000 INFO @ Tue, 16 Jun 2020 08:53:22: 13000000 INFO @ Tue, 16 Jun 2020 08:53:23: 17000000 INFO @ Tue, 16 Jun 2020 08:53:24: 20000000 INFO @ Tue, 16 Jun 2020 08:53:30: 14000000 INFO @ Tue, 16 Jun 2020 08:53:31: 18000000 INFO @ Tue, 16 Jun 2020 08:53:33: 21000000 INFO @ Tue, 16 Jun 2020 08:53:38: 15000000 INFO @ Tue, 16 Jun 2020 08:53:39: 19000000 INFO @ Tue, 16 Jun 2020 08:53:41: 22000000 INFO @ Tue, 16 Jun 2020 08:53:46: 16000000 INFO @ Tue, 16 Jun 2020 08:53:47: 20000000 INFO @ Tue, 16 Jun 2020 08:53:50: 23000000 INFO @ Tue, 16 Jun 2020 08:53:54: 17000000 INFO @ Tue, 16 Jun 2020 08:53:55: 21000000 INFO @ Tue, 16 Jun 2020 08:53:59: 24000000 INFO @ Tue, 16 Jun 2020 08:54:02: 18000000 INFO @ Tue, 16 Jun 2020 08:54:03: 22000000 INFO @ Tue, 16 Jun 2020 08:54:07: 25000000 INFO @ Tue, 16 Jun 2020 08:54:10: 19000000 INFO @ Tue, 16 Jun 2020 08:54:11: 23000000 INFO @ Tue, 16 Jun 2020 08:54:16: 26000000 INFO @ Tue, 16 Jun 2020 08:54:18: 20000000 INFO @ Tue, 16 Jun 2020 08:54:19: 24000000 INFO @ Tue, 16 Jun 2020 08:54:24: 27000000 INFO @ Tue, 16 Jun 2020 08:54:26: 21000000 INFO @ Tue, 16 Jun 2020 08:54:27: 25000000 INFO @ Tue, 16 Jun 2020 08:54:33: 28000000 INFO @ Tue, 16 Jun 2020 08:54:34: 22000000 INFO @ Tue, 16 Jun 2020 08:54:35: 26000000 INFO @ Tue, 16 Jun 2020 08:54:42: 29000000 INFO @ Tue, 16 Jun 2020 08:54:42: 23000000 INFO @ Tue, 16 Jun 2020 08:54:43: 27000000 INFO @ Tue, 16 Jun 2020 08:54:50: 24000000 INFO @ Tue, 16 Jun 2020 08:54:51: 30000000 INFO @ Tue, 16 Jun 2020 08:54:51: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:54:58: 25000000 INFO @ Tue, 16 Jun 2020 08:54:59: 31000000 INFO @ Tue, 16 Jun 2020 08:54:59: 29000000 INFO @ Tue, 16 Jun 2020 08:55:06: 26000000 INFO @ Tue, 16 Jun 2020 08:55:08: 30000000 INFO @ Tue, 16 Jun 2020 08:55:08: 32000000 INFO @ Tue, 16 Jun 2020 08:55:14: 27000000 INFO @ Tue, 16 Jun 2020 08:55:16: 31000000 INFO @ Tue, 16 Jun 2020 08:55:17: 33000000 INFO @ Tue, 16 Jun 2020 08:55:21: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:55:21: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:55:21: #1 total tags in treatment: 16582716 INFO @ Tue, 16 Jun 2020 08:55:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:55:21: #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 08:55:21: #1 tags after filtering in treatment: 14856676 INFO @ Tue, 16 Jun 2020 08:55:21: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 16 Jun 2020 08:55:21: #1 finished! INFO @ Tue, 16 Jun 2020 08:55:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:55:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:55:22: 28000000 INFO @ Tue, 16 Jun 2020 08:55:22: #2 number of paired peaks: 267 WARNING @ Tue, 16 Jun 2020 08:55:22: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Tue, 16 Jun 2020 08:55:22: start model_add_line... INFO @ Tue, 16 Jun 2020 08:55:22: start X-correlation... INFO @ Tue, 16 Jun 2020 08:55:22: end of X-cor INFO @ Tue, 16 Jun 2020 08:55:22: #2 finished! INFO @ Tue, 16 Jun 2020 08:55:22: #2 predicted fragment length is 170 bps INFO @ Tue, 16 Jun 2020 08:55:22: #2 alternative fragment length(s) may be 170 bps INFO @ Tue, 16 Jun 2020 08:55:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/ERX1485062/ERX1485062.05_model.r WARNING @ Tue, 16 Jun 2020 08:55:22: #2 Since the d (170) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:55:22: #2 You may need to consider one of the other alternative d(s): 170 WARNING @ Tue, 16 Jun 2020 08:55:22: #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 08:55:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:55:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:55:24: 32000000 INFO @ Tue, 16 Jun 2020 08:55:30: 29000000 INFO @ Tue, 16 Jun 2020 08:55:31: 33000000 INFO @ Tue, 16 Jun 2020 08:55:35: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:55:35: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:55:35: #1 total tags in treatment: 16582716 INFO @ Tue, 16 Jun 2020 08:55:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:55:35: #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 08:55:36: #1 tags after filtering in treatment: 14856676 INFO @ Tue, 16 Jun 2020 08:55:36: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 16 Jun 2020 08:55:36: #1 finished! INFO @ Tue, 16 Jun 2020 08:55:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:55:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:55:37: #2 number of paired peaks: 267 WARNING @ Tue, 16 Jun 2020 08:55:37: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Tue, 16 Jun 2020 08:55:37: start model_add_line... INFO @ Tue, 16 Jun 2020 08:55:37: start X-correlation... INFO @ Tue, 16 Jun 2020 08:55:37: end of X-cor INFO @ Tue, 16 Jun 2020 08:55:37: #2 finished! INFO @ Tue, 16 Jun 2020 08:55:37: #2 predicted fragment length is 170 bps INFO @ Tue, 16 Jun 2020 08:55:37: #2 alternative fragment length(s) may be 170 bps INFO @ Tue, 16 Jun 2020 08:55:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/ERX1485062/ERX1485062.10_model.r WARNING @ Tue, 16 Jun 2020 08:55:37: #2 Since the d (170) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:55:37: #2 You may need to consider one of the other alternative d(s): 170 WARNING @ Tue, 16 Jun 2020 08:55:37: #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 08:55:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:55:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:55:38: 30000000 INFO @ Tue, 16 Jun 2020 08:55:45: 31000000 INFO @ Tue, 16 Jun 2020 08:55:52: 32000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:55:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:56:00: 33000000 INFO @ Tue, 16 Jun 2020 08:56:03: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:56:03: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:56:03: #1 total tags in treatment: 16582716 INFO @ Tue, 16 Jun 2020 08:56:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:56:03: #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 08:56:04: #1 tags after filtering in treatment: 14856676 INFO @ Tue, 16 Jun 2020 08:56:04: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 16 Jun 2020 08:56:04: #1 finished! INFO @ Tue, 16 Jun 2020 08:56:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:56:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:56:05: #2 number of paired peaks: 267 WARNING @ Tue, 16 Jun 2020 08:56:05: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Tue, 16 Jun 2020 08:56:05: start model_add_line... INFO @ Tue, 16 Jun 2020 08:56:05: start X-correlation... INFO @ Tue, 16 Jun 2020 08:56:05: end of X-cor INFO @ Tue, 16 Jun 2020 08:56:05: #2 finished! INFO @ Tue, 16 Jun 2020 08:56:05: #2 predicted fragment length is 170 bps INFO @ Tue, 16 Jun 2020 08:56:05: #2 alternative fragment length(s) may be 170 bps INFO @ Tue, 16 Jun 2020 08:56:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/ERX1485062/ERX1485062.20_model.r WARNING @ Tue, 16 Jun 2020 08:56:05: #2 Since the d (170) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:56:05: #2 You may need to consider one of the other alternative d(s): 170 WARNING @ Tue, 16 Jun 2020 08:56:05: #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 08:56:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:56:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:56:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/ERX1485062/ERX1485062.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:56:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/ERX1485062/ERX1485062.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:56:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/ERX1485062/ERX1485062.05_summits.bed INFO @ Tue, 16 Jun 2020 08:56:11: Done! INFO @ Tue, 16 Jun 2020 08:56:11: #3 Call peaks for each chromosome... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5821 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:56:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/ERX1485062/ERX1485062.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:56:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/ERX1485062/ERX1485062.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:56:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/ERX1485062/ERX1485062.10_summits.bed INFO @ Tue, 16 Jun 2020 08:56:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3531 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:56:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:56:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/ERX1485062/ERX1485062.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:56:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/ERX1485062/ERX1485062.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:56:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/ERX1485062/ERX1485062.20_summits.bed INFO @ Tue, 16 Jun 2020 08:56:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1658 records, 4 fields): 3 millis CompletedMACS2peakCalling