Job ID = 6367846 SRX = SRX4085414 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-16T00:11:50 prefetch.2.10.7: 1) Downloading 'SRR7167443'... 2020-06-16T00:11:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:16:37 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:16:37 prefetch.2.10.7: 1) 'SRR7167443' was downloaded successfully Read 15304005 spots for SRR7167443/SRR7167443.sra Written 15304005 spots for SRR7167443/SRR7167443.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: 00:10:02 15304005 reads; of these: 15304005 (100.00%) were paired; of these: 10353193 (67.65%) aligned concordantly 0 times 4170108 (27.25%) aligned concordantly exactly 1 time 780704 (5.10%) aligned concordantly >1 times ---- 10353193 pairs aligned concordantly 0 times; of these: 245836 (2.37%) aligned discordantly 1 time ---- 10107357 pairs aligned 0 times concordantly or discordantly; of these: 20214714 mates make up the pairs; of these: 14398636 (71.23%) aligned 0 times 5167411 (25.56%) aligned exactly 1 time 648667 (3.21%) aligned >1 times 52.96% overall alignment rate Time searching: 00:10:02 Overall time: 00:10:02 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 8 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] 421326 / 5078804 = 0.0830 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 09:34:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085414/SRX4085414.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085414/SRX4085414.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085414/SRX4085414.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085414/SRX4085414.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 09:34:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:32: 1000000 INFO @ Tue, 16 Jun 2020 09:34:38: 2000000 INFO @ Tue, 16 Jun 2020 09:34:45: 3000000 INFO @ Tue, 16 Jun 2020 09:34:51: 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 09:34:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085414/SRX4085414.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085414/SRX4085414.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085414/SRX4085414.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085414/SRX4085414.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 09:34:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:58: 5000000 INFO @ Tue, 16 Jun 2020 09:35:03: 1000000 INFO @ Tue, 16 Jun 2020 09:35:05: 6000000 INFO @ Tue, 16 Jun 2020 09:35:11: 2000000 INFO @ Tue, 16 Jun 2020 09:35:13: 7000000 INFO @ Tue, 16 Jun 2020 09:35:18: 3000000 INFO @ Tue, 16 Jun 2020 09:35:20: 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 09:35:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085414/SRX4085414.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085414/SRX4085414.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085414/SRX4085414.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085414/SRX4085414.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 09:35:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:35:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:35:26: 4000000 INFO @ Tue, 16 Jun 2020 09:35:28: 9000000 INFO @ Tue, 16 Jun 2020 09:35:32: 1000000 INFO @ Tue, 16 Jun 2020 09:35:35: 5000000 INFO @ Tue, 16 Jun 2020 09:35:37: 10000000 INFO @ Tue, 16 Jun 2020 09:35:39: 2000000 INFO @ Tue, 16 Jun 2020 09:35:43: 6000000 INFO @ Tue, 16 Jun 2020 09:35:45: 3000000 INFO @ Tue, 16 Jun 2020 09:35:46: 11000000 INFO @ Tue, 16 Jun 2020 09:35:52: 4000000 INFO @ Tue, 16 Jun 2020 09:35:52: 7000000 INFO @ Tue, 16 Jun 2020 09:35:55: 12000000 INFO @ Tue, 16 Jun 2020 09:35:58: 5000000 INFO @ Tue, 16 Jun 2020 09:36:01: 8000000 INFO @ Tue, 16 Jun 2020 09:36:03: 13000000 INFO @ Tue, 16 Jun 2020 09:36:07: 6000000 INFO @ Tue, 16 Jun 2020 09:36:10: 9000000 INFO @ Tue, 16 Jun 2020 09:36:12: 14000000 INFO @ Tue, 16 Jun 2020 09:36:16: 7000000 INFO @ Tue, 16 Jun 2020 09:36:18: 10000000 INFO @ Tue, 16 Jun 2020 09:36:20: 15000000 INFO @ Tue, 16 Jun 2020 09:36:22: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:36:22: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:36:22: #1 total tags in treatment: 4539284 INFO @ Tue, 16 Jun 2020 09:36:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:22: #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 09:36:22: #1 tags after filtering in treatment: 3980672 INFO @ Tue, 16 Jun 2020 09:36:22: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 16 Jun 2020 09:36:22: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:23: #2 number of paired peaks: 828 WARNING @ Tue, 16 Jun 2020 09:36:23: Fewer paired peaks (828) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 828 pairs to build model! INFO @ Tue, 16 Jun 2020 09:36:23: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:23: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:23: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:23: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:23: #2 predicted fragment length is 80 bps INFO @ Tue, 16 Jun 2020 09:36:23: #2 alternative fragment length(s) may be 80 bps INFO @ Tue, 16 Jun 2020 09:36:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085414/SRX4085414.05_model.r WARNING @ Tue, 16 Jun 2020 09:36:23: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:36:23: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Tue, 16 Jun 2020 09:36:23: #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 09:36:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:36:25: 8000000 INFO @ Tue, 16 Jun 2020 09:36:27: 11000000 INFO @ Tue, 16 Jun 2020 09:36:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:36:35: 9000000 INFO @ Tue, 16 Jun 2020 09:36:35: 12000000 INFO @ Tue, 16 Jun 2020 09:36:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085414/SRX4085414.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085414/SRX4085414.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085414/SRX4085414.05_summits.bed INFO @ Tue, 16 Jun 2020 09:36:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4369 records, 4 fields): 111 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:36:43: 13000000 INFO @ Tue, 16 Jun 2020 09:36:44: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:36:51: 14000000 INFO @ Tue, 16 Jun 2020 09:36:53: 11000000 INFO @ Tue, 16 Jun 2020 09:36:59: 15000000 INFO @ Tue, 16 Jun 2020 09:37:02: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:37:02: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:37:02: #1 total tags in treatment: 4539284 INFO @ Tue, 16 Jun 2020 09:37:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:37:02: #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 09:37:02: #1 tags after filtering in treatment: 3980672 INFO @ Tue, 16 Jun 2020 09:37:02: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 16 Jun 2020 09:37:02: #1 finished! INFO @ Tue, 16 Jun 2020 09:37:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:37:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:37:02: #2 number of paired peaks: 828 WARNING @ Tue, 16 Jun 2020 09:37:02: Fewer paired peaks (828) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 828 pairs to build model! INFO @ Tue, 16 Jun 2020 09:37:02: start model_add_line... INFO @ Tue, 16 Jun 2020 09:37:02: start X-correlation... INFO @ Tue, 16 Jun 2020 09:37:02: end of X-cor INFO @ Tue, 16 Jun 2020 09:37:02: #2 finished! INFO @ Tue, 16 Jun 2020 09:37:02: #2 predicted fragment length is 80 bps INFO @ Tue, 16 Jun 2020 09:37:02: #2 alternative fragment length(s) may be 80 bps INFO @ Tue, 16 Jun 2020 09:37:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085414/SRX4085414.10_model.r WARNING @ Tue, 16 Jun 2020 09:37:02: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:37:02: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Tue, 16 Jun 2020 09:37:02: #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 09:37:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:37:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:37:03: 12000000 INFO @ Tue, 16 Jun 2020 09:37:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:37:12: 13000000 INFO @ Tue, 16 Jun 2020 09:37:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085414/SRX4085414.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:37:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085414/SRX4085414.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:37:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085414/SRX4085414.10_summits.bed INFO @ Tue, 16 Jun 2020 09:37:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2344 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:37:21: 14000000 INFO @ Tue, 16 Jun 2020 09:37:30: 15000000 INFO @ Tue, 16 Jun 2020 09:37:33: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:37:33: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:37:33: #1 total tags in treatment: 4539284 INFO @ Tue, 16 Jun 2020 09:37:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:37:33: #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 09:37:33: #1 tags after filtering in treatment: 3980672 INFO @ Tue, 16 Jun 2020 09:37:33: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 16 Jun 2020 09:37:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:37:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:37:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:37:34: #2 number of paired peaks: 828 WARNING @ Tue, 16 Jun 2020 09:37:34: Fewer paired peaks (828) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 828 pairs to build model! INFO @ Tue, 16 Jun 2020 09:37:34: start model_add_line... INFO @ Tue, 16 Jun 2020 09:37:34: start X-correlation... INFO @ Tue, 16 Jun 2020 09:37:34: end of X-cor INFO @ Tue, 16 Jun 2020 09:37:34: #2 finished! INFO @ Tue, 16 Jun 2020 09:37:34: #2 predicted fragment length is 80 bps INFO @ Tue, 16 Jun 2020 09:37:34: #2 alternative fragment length(s) may be 80 bps INFO @ Tue, 16 Jun 2020 09:37:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085414/SRX4085414.20_model.r WARNING @ Tue, 16 Jun 2020 09:37:34: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:37:34: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Tue, 16 Jun 2020 09:37:34: #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 09:37:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:37:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:37:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:37:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085414/SRX4085414.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:37:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085414/SRX4085414.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:37:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085414/SRX4085414.20_summits.bed INFO @ Tue, 16 Jun 2020 09:37:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (846 records, 4 fields): 22 millis CompletedMACS2peakCalling