Job ID = 6507744 SRX = SRX2011722 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T13:51:57 prefetch.2.10.7: 1) Downloading 'SRR4017964'... 2020-06-26T13:51:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:58:07 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:58:07 prefetch.2.10.7: 1) 'SRR4017964' was downloaded successfully Read 17446004 spots for SRR4017964/SRR4017964.sra Written 17446004 spots for SRR4017964/SRR4017964.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:23:24 17446004 reads; of these: 17446004 (100.00%) were paired; of these: 2002848 (11.48%) aligned concordantly 0 times 13683399 (78.43%) aligned concordantly exactly 1 time 1759757 (10.09%) aligned concordantly >1 times ---- 2002848 pairs aligned concordantly 0 times; of these: 1250013 (62.41%) aligned discordantly 1 time ---- 752835 pairs aligned 0 times concordantly or discordantly; of these: 1505670 mates make up the pairs; of these: 982324 (65.24%) aligned 0 times 231066 (15.35%) aligned exactly 1 time 292280 (19.41%) aligned >1 times 97.18% overall alignment rate Time searching: 00:23:25 Overall time: 00:23:25 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 16 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] 4018325 / 16620645 = 0.2418 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 @ Fri, 26 Jun 2020 23:38:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2011722/SRX2011722.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2011722/SRX2011722.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2011722/SRX2011722.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2011722/SRX2011722.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 @ Fri, 26 Jun 2020 23:38:17: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:38:17: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:38:23: 1000000 INFO @ Fri, 26 Jun 2020 23:38:30: 2000000 INFO @ Fri, 26 Jun 2020 23:38:36: 3000000 INFO @ Fri, 26 Jun 2020 23:38:42: 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 @ Fri, 26 Jun 2020 23:38:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2011722/SRX2011722.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2011722/SRX2011722.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2011722/SRX2011722.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2011722/SRX2011722.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 @ Fri, 26 Jun 2020 23:38:47: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:38:47: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:38:49: 5000000 INFO @ Fri, 26 Jun 2020 23:38:54: 1000000 INFO @ Fri, 26 Jun 2020 23:38:55: 6000000 INFO @ Fri, 26 Jun 2020 23:39:01: 2000000 INFO @ Fri, 26 Jun 2020 23:39:02: 7000000 INFO @ Fri, 26 Jun 2020 23:39:08: 3000000 INFO @ Fri, 26 Jun 2020 23:39:09: 8000000 INFO @ Fri, 26 Jun 2020 23:39:14: 4000000 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 @ Fri, 26 Jun 2020 23:39:16: 9000000 INFO @ Fri, 26 Jun 2020 23:39:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2011722/SRX2011722.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2011722/SRX2011722.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2011722/SRX2011722.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2011722/SRX2011722.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 @ Fri, 26 Jun 2020 23:39:17: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:39:17: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:39:22: 5000000 INFO @ Fri, 26 Jun 2020 23:39:23: 10000000 INFO @ Fri, 26 Jun 2020 23:39:26: 1000000 INFO @ Fri, 26 Jun 2020 23:39:29: 6000000 INFO @ Fri, 26 Jun 2020 23:39:31: 11000000 INFO @ Fri, 26 Jun 2020 23:39:35: 2000000 INFO @ Fri, 26 Jun 2020 23:39:37: 7000000 INFO @ Fri, 26 Jun 2020 23:39:38: 12000000 INFO @ Fri, 26 Jun 2020 23:39:43: 3000000 INFO @ Fri, 26 Jun 2020 23:39:44: 8000000 INFO @ Fri, 26 Jun 2020 23:39:46: 13000000 INFO @ Fri, 26 Jun 2020 23:39:52: 9000000 INFO @ Fri, 26 Jun 2020 23:39:52: 4000000 INFO @ Fri, 26 Jun 2020 23:39:54: 14000000 INFO @ Fri, 26 Jun 2020 23:39:59: 10000000 INFO @ Fri, 26 Jun 2020 23:40:01: 5000000 INFO @ Fri, 26 Jun 2020 23:40:01: 15000000 INFO @ Fri, 26 Jun 2020 23:40:07: 11000000 INFO @ Fri, 26 Jun 2020 23:40:09: 16000000 INFO @ Fri, 26 Jun 2020 23:40:09: 6000000 INFO @ Fri, 26 Jun 2020 23:40:15: 12000000 INFO @ Fri, 26 Jun 2020 23:40:16: 17000000 INFO @ Fri, 26 Jun 2020 23:40:18: 7000000 INFO @ Fri, 26 Jun 2020 23:40:22: 13000000 INFO @ Fri, 26 Jun 2020 23:40:24: 18000000 INFO @ Fri, 26 Jun 2020 23:40:27: 8000000 INFO @ Fri, 26 Jun 2020 23:40:30: 14000000 INFO @ Fri, 26 Jun 2020 23:40:32: 19000000 INFO @ Fri, 26 Jun 2020 23:40:36: 9000000 INFO @ Fri, 26 Jun 2020 23:40:37: 15000000 INFO @ Fri, 26 Jun 2020 23:40:39: 20000000 INFO @ Fri, 26 Jun 2020 23:40:45: 10000000 INFO @ Fri, 26 Jun 2020 23:40:45: 16000000 INFO @ Fri, 26 Jun 2020 23:40:47: 21000000 INFO @ Fri, 26 Jun 2020 23:40:52: 17000000 INFO @ Fri, 26 Jun 2020 23:40:53: 11000000 INFO @ Fri, 26 Jun 2020 23:40:55: 22000000 INFO @ Fri, 26 Jun 2020 23:41:00: 18000000 INFO @ Fri, 26 Jun 2020 23:41:02: 12000000 INFO @ Fri, 26 Jun 2020 23:41:02: 23000000 INFO @ Fri, 26 Jun 2020 23:41:08: 19000000 INFO @ Fri, 26 Jun 2020 23:41:10: 24000000 INFO @ Fri, 26 Jun 2020 23:41:11: 13000000 INFO @ Fri, 26 Jun 2020 23:41:15: 20000000 INFO @ Fri, 26 Jun 2020 23:41:18: 25000000 INFO @ Fri, 26 Jun 2020 23:41:19: 14000000 INFO @ Fri, 26 Jun 2020 23:41:23: 21000000 INFO @ Fri, 26 Jun 2020 23:41:24: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 23:41:24: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 23:41:24: #1 total tags in treatment: 11613280 INFO @ Fri, 26 Jun 2020 23:41:24: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:41:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:41:25: #1 tags after filtering in treatment: 10315258 INFO @ Fri, 26 Jun 2020 23:41:25: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 26 Jun 2020 23:41:25: #1 finished! INFO @ Fri, 26 Jun 2020 23:41:25: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:41:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:41:25: #2 number of paired peaks: 1859 INFO @ Fri, 26 Jun 2020 23:41:25: start model_add_line... INFO @ Fri, 26 Jun 2020 23:41:26: start X-correlation... INFO @ Fri, 26 Jun 2020 23:41:26: end of X-cor INFO @ Fri, 26 Jun 2020 23:41:26: #2 finished! INFO @ Fri, 26 Jun 2020 23:41:26: #2 predicted fragment length is 175 bps INFO @ Fri, 26 Jun 2020 23:41:26: #2 alternative fragment length(s) may be 4,175 bps INFO @ Fri, 26 Jun 2020 23:41:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2011722/SRX2011722.05_model.r WARNING @ Fri, 26 Jun 2020 23:41:26: #2 Since the d (175) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:41:26: #2 You may need to consider one of the other alternative d(s): 4,175 WARNING @ Fri, 26 Jun 2020 23:41:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:41:26: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:41:26: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:41:28: 15000000 INFO @ Fri, 26 Jun 2020 23:41:30: 22000000 INFO @ Fri, 26 Jun 2020 23:41:36: 16000000 INFO @ Fri, 26 Jun 2020 23:41:38: 23000000 INFO @ Fri, 26 Jun 2020 23:41:44: 17000000 INFO @ Fri, 26 Jun 2020 23:41:45: 24000000 INFO @ Fri, 26 Jun 2020 23:41:52: 25000000 INFO @ Fri, 26 Jun 2020 23:41:53: 18000000 INFO @ Fri, 26 Jun 2020 23:41:55: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:41:58: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 23:41:58: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 23:41:58: #1 total tags in treatment: 11613280 INFO @ Fri, 26 Jun 2020 23:41:58: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:41:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:41:59: #1 tags after filtering in treatment: 10315258 INFO @ Fri, 26 Jun 2020 23:41:59: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 26 Jun 2020 23:41:59: #1 finished! INFO @ Fri, 26 Jun 2020 23:41:59: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:41:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:41:59: #2 number of paired peaks: 1859 INFO @ Fri, 26 Jun 2020 23:41:59: start model_add_line... INFO @ Fri, 26 Jun 2020 23:42:00: start X-correlation... INFO @ Fri, 26 Jun 2020 23:42:00: end of X-cor INFO @ Fri, 26 Jun 2020 23:42:00: #2 finished! INFO @ Fri, 26 Jun 2020 23:42:00: #2 predicted fragment length is 175 bps INFO @ Fri, 26 Jun 2020 23:42:00: #2 alternative fragment length(s) may be 4,175 bps INFO @ Fri, 26 Jun 2020 23:42:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2011722/SRX2011722.10_model.r WARNING @ Fri, 26 Jun 2020 23:42:00: #2 Since the d (175) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:42:00: #2 You may need to consider one of the other alternative d(s): 4,175 WARNING @ Fri, 26 Jun 2020 23:42:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:42:00: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:42:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:42:01: 19000000 INFO @ Fri, 26 Jun 2020 23:42:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2011722/SRX2011722.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:42:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2011722/SRX2011722.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:42:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2011722/SRX2011722.05_summits.bed INFO @ Fri, 26 Jun 2020 23:42:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4759 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:42:09: 20000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:42:17: 21000000 INFO @ Fri, 26 Jun 2020 23:42:25: 22000000 INFO @ Fri, 26 Jun 2020 23:42:28: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:42:32: 23000000 INFO @ Fri, 26 Jun 2020 23:42:40: 24000000 INFO @ Fri, 26 Jun 2020 23:42:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2011722/SRX2011722.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:42:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2011722/SRX2011722.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:42:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2011722/SRX2011722.10_summits.bed INFO @ Fri, 26 Jun 2020 23:42:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2812 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:42:48: 25000000 INFO @ Fri, 26 Jun 2020 23:42:55: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 23:42:55: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 23:42:55: #1 total tags in treatment: 11613280 INFO @ Fri, 26 Jun 2020 23:42:55: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:42:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:42:55: #1 tags after filtering in treatment: 10315258 INFO @ Fri, 26 Jun 2020 23:42:55: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 26 Jun 2020 23:42:55: #1 finished! INFO @ Fri, 26 Jun 2020 23:42:55: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:42:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:42:56: #2 number of paired peaks: 1859 INFO @ Fri, 26 Jun 2020 23:42:56: start model_add_line... INFO @ Fri, 26 Jun 2020 23:42:56: start X-correlation... INFO @ Fri, 26 Jun 2020 23:42:56: end of X-cor INFO @ Fri, 26 Jun 2020 23:42:56: #2 finished! INFO @ Fri, 26 Jun 2020 23:42:56: #2 predicted fragment length is 175 bps INFO @ Fri, 26 Jun 2020 23:42:56: #2 alternative fragment length(s) may be 4,175 bps INFO @ Fri, 26 Jun 2020 23:42:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2011722/SRX2011722.20_model.r WARNING @ Fri, 26 Jun 2020 23:42:56: #2 Since the d (175) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:42:56: #2 You may need to consider one of the other alternative d(s): 4,175 WARNING @ Fri, 26 Jun 2020 23:42:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:42:56: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:42:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:43:24: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:43:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2011722/SRX2011722.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:43:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2011722/SRX2011722.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:43:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2011722/SRX2011722.20_summits.bed INFO @ Fri, 26 Jun 2020 23:43:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1140 records, 4 fields): 2 millis CompletedMACS2peakCalling