Job ID = 6367849 SRX = SRX4085417 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:48:50 prefetch.2.10.7: 1) Downloading 'SRR7167446'... 2020-06-15T23:48:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:52:12 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:52:12 prefetch.2.10.7: 1) 'SRR7167446' was downloaded successfully Read 14395633 spots for SRR7167446/SRR7167446.sra Written 14395633 spots for SRR7167446/SRR7167446.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: 00:07:43 14395633 reads; of these: 14395633 (100.00%) were paired; of these: 11446088 (79.51%) aligned concordantly 0 times 2502152 (17.38%) aligned concordantly exactly 1 time 447393 (3.11%) aligned concordantly >1 times ---- 11446088 pairs aligned concordantly 0 times; of these: 344003 (3.01%) aligned discordantly 1 time ---- 11102085 pairs aligned 0 times concordantly or discordantly; of these: 22204170 mates make up the pairs; of these: 16139065 (72.68%) aligned 0 times 5230176 (23.55%) aligned exactly 1 time 834929 (3.76%) aligned >1 times 43.94% overall alignment rate Time searching: 00:07:43 Overall time: 00:07:43 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] 147758 / 3127889 = 0.0472 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 09:05:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085417/SRX4085417.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085417/SRX4085417.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085417/SRX4085417.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085417/SRX4085417.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 09:05:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:05:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:05:50: 1000000 INFO @ Tue, 16 Jun 2020 09:05:57: 2000000 INFO @ Tue, 16 Jun 2020 09:06:03: 3000000 INFO @ Tue, 16 Jun 2020 09:06:10: 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 09:06:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085417/SRX4085417.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085417/SRX4085417.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085417/SRX4085417.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085417/SRX4085417.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 09:06:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:06:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:06:18: 5000000 INFO @ Tue, 16 Jun 2020 09:06:20: 1000000 INFO @ Tue, 16 Jun 2020 09:06:25: 6000000 INFO @ Tue, 16 Jun 2020 09:06:28: 2000000 INFO @ Tue, 16 Jun 2020 09:06:33: 7000000 INFO @ Tue, 16 Jun 2020 09:06:36: 3000000 INFO @ Tue, 16 Jun 2020 09:06:40: 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 09:06:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085417/SRX4085417.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085417/SRX4085417.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085417/SRX4085417.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085417/SRX4085417.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 09:06:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:06:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:06:43: 4000000 INFO @ Tue, 16 Jun 2020 09:06:48: 9000000 INFO @ Tue, 16 Jun 2020 09:06:51: 1000000 INFO @ Tue, 16 Jun 2020 09:06:51: 5000000 INFO @ Tue, 16 Jun 2020 09:06:55: 10000000 INFO @ Tue, 16 Jun 2020 09:06:59: 2000000 INFO @ Tue, 16 Jun 2020 09:06:59: 6000000 INFO @ Tue, 16 Jun 2020 09:07:03: 11000000 INFO @ Tue, 16 Jun 2020 09:07:06: 3000000 INFO @ Tue, 16 Jun 2020 09:07:06: 7000000 INFO @ Tue, 16 Jun 2020 09:07:10: 12000000 INFO @ Tue, 16 Jun 2020 09:07:13: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:07:13: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:07:13: #1 total tags in treatment: 2809169 INFO @ Tue, 16 Jun 2020 09:07:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:07:13: #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 09:07:13: #1 tags after filtering in treatment: 2689761 INFO @ Tue, 16 Jun 2020 09:07:13: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 16 Jun 2020 09:07:13: #1 finished! INFO @ Tue, 16 Jun 2020 09:07:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:07:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:07:13: 4000000 INFO @ Tue, 16 Jun 2020 09:07:13: 8000000 INFO @ Tue, 16 Jun 2020 09:07:13: #2 number of paired peaks: 363 WARNING @ Tue, 16 Jun 2020 09:07:13: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Tue, 16 Jun 2020 09:07:13: start model_add_line... INFO @ Tue, 16 Jun 2020 09:07:13: start X-correlation... INFO @ Tue, 16 Jun 2020 09:07:13: end of X-cor INFO @ Tue, 16 Jun 2020 09:07:13: #2 finished! INFO @ Tue, 16 Jun 2020 09:07:13: #2 predicted fragment length is 195 bps INFO @ Tue, 16 Jun 2020 09:07:13: #2 alternative fragment length(s) may be 95,128,165,195,225 bps INFO @ Tue, 16 Jun 2020 09:07:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085417/SRX4085417.05_model.r INFO @ Tue, 16 Jun 2020 09:07:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:07:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:07:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:07:20: 5000000 INFO @ Tue, 16 Jun 2020 09:07:21: 9000000 INFO @ Tue, 16 Jun 2020 09:07:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085417/SRX4085417.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:07:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085417/SRX4085417.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:07:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085417/SRX4085417.05_summits.bed INFO @ Tue, 16 Jun 2020 09:07:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (215 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:07:28: 10000000 INFO @ Tue, 16 Jun 2020 09:07:28: 6000000 INFO @ Tue, 16 Jun 2020 09:07:35: 11000000 INFO @ Tue, 16 Jun 2020 09:07:35: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:07:42: 12000000 INFO @ Tue, 16 Jun 2020 09:07:43: 8000000 INFO @ Tue, 16 Jun 2020 09:07:45: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:07:45: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:07:45: #1 total tags in treatment: 2809169 INFO @ Tue, 16 Jun 2020 09:07:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:07:45: #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 09:07:45: #1 tags after filtering in treatment: 2689761 INFO @ Tue, 16 Jun 2020 09:07:45: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 16 Jun 2020 09:07:45: #1 finished! INFO @ Tue, 16 Jun 2020 09:07:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:07:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:07:45: #2 number of paired peaks: 363 WARNING @ Tue, 16 Jun 2020 09:07:45: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Tue, 16 Jun 2020 09:07:45: start model_add_line... INFO @ Tue, 16 Jun 2020 09:07:45: start X-correlation... INFO @ Tue, 16 Jun 2020 09:07:45: end of X-cor INFO @ Tue, 16 Jun 2020 09:07:45: #2 finished! INFO @ Tue, 16 Jun 2020 09:07:45: #2 predicted fragment length is 195 bps INFO @ Tue, 16 Jun 2020 09:07:45: #2 alternative fragment length(s) may be 95,128,165,195,225 bps INFO @ Tue, 16 Jun 2020 09:07:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085417/SRX4085417.10_model.r INFO @ Tue, 16 Jun 2020 09:07:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:07:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:07:50: 9000000 INFO @ Tue, 16 Jun 2020 09:07:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:07:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085417/SRX4085417.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:07:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085417/SRX4085417.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:07:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085417/SRX4085417.10_summits.bed INFO @ Tue, 16 Jun 2020 09:07:55: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (151 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:07:57: 10000000 INFO @ Tue, 16 Jun 2020 09:08:03: 11000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:08:10: 12000000 INFO @ Tue, 16 Jun 2020 09:08:13: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:08:13: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:08:13: #1 total tags in treatment: 2809169 INFO @ Tue, 16 Jun 2020 09:08:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:08:13: #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 09:08:13: #1 tags after filtering in treatment: 2689761 INFO @ Tue, 16 Jun 2020 09:08:13: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 16 Jun 2020 09:08:13: #1 finished! INFO @ Tue, 16 Jun 2020 09:08:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:08:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:08:13: #2 number of paired peaks: 363 WARNING @ Tue, 16 Jun 2020 09:08:13: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Tue, 16 Jun 2020 09:08:13: start model_add_line... INFO @ Tue, 16 Jun 2020 09:08:13: start X-correlation... INFO @ Tue, 16 Jun 2020 09:08:13: end of X-cor INFO @ Tue, 16 Jun 2020 09:08:13: #2 finished! INFO @ Tue, 16 Jun 2020 09:08:13: #2 predicted fragment length is 195 bps INFO @ Tue, 16 Jun 2020 09:08:13: #2 alternative fragment length(s) may be 95,128,165,195,225 bps INFO @ Tue, 16 Jun 2020 09:08:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085417/SRX4085417.20_model.r INFO @ Tue, 16 Jun 2020 09:08:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:08:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:08:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:08:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085417/SRX4085417.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:08:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085417/SRX4085417.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:08:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085417/SRX4085417.20_summits.bed INFO @ Tue, 16 Jun 2020 09:08:22: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (85 records, 4 fields): 1 millis CompletedMACS2peakCalling