Job ID = 6497354 SRX = SRX2011722 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T22:10:26 prefetch.2.10.7: 1) Downloading 'SRR4017964'... 2020-06-25T22:10:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:17:24 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:17:24 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:23:03 17446004 reads; of these: 17446004 (100.00%) were paired; of these: 2002864 (11.48%) aligned concordantly 0 times 13683446 (78.43%) aligned concordantly exactly 1 time 1759694 (10.09%) aligned concordantly >1 times ---- 2002864 pairs aligned concordantly 0 times; of these: 1249978 (62.41%) aligned discordantly 1 time ---- 752886 pairs aligned 0 times concordantly or discordantly; of these: 1505772 mates make up the pairs; of these: 982407 (65.24%) aligned 0 times 231090 (15.35%) aligned exactly 1 time 292275 (19.41%) aligned >1 times 97.18% overall alignment rate Time searching: 00:23:03 Overall time: 00:23:03 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] 4018290 / 16620592 = 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 07:57:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2011722/SRX2011722.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2011722/SRX2011722.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2011722/SRX2011722.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 07:57:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:57:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:58:02: 1000000 INFO @ Fri, 26 Jun 2020 07:58:09: 2000000 INFO @ Fri, 26 Jun 2020 07:58:16: 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 @ Fri, 26 Jun 2020 07:58:23: 4000000 INFO @ Fri, 26 Jun 2020 07:58:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2011722/SRX2011722.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2011722/SRX2011722.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2011722/SRX2011722.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 07:58:25: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:58:25: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:58:31: 5000000 INFO @ Fri, 26 Jun 2020 07:58:33: 1000000 INFO @ Fri, 26 Jun 2020 07:58:38: 6000000 INFO @ Fri, 26 Jun 2020 07:58:40: 2000000 INFO @ Fri, 26 Jun 2020 07:58:46: 7000000 INFO @ Fri, 26 Jun 2020 07:58:48: 3000000 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 07:58:54: 8000000 INFO @ Fri, 26 Jun 2020 07:58:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2011722/SRX2011722.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2011722/SRX2011722.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2011722/SRX2011722.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 07:58:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:58:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:58:56: 4000000 INFO @ Fri, 26 Jun 2020 07:59:01: 9000000 INFO @ Fri, 26 Jun 2020 07:59:03: 1000000 INFO @ Fri, 26 Jun 2020 07:59:03: 5000000 INFO @ Fri, 26 Jun 2020 07:59:09: 10000000 INFO @ Fri, 26 Jun 2020 07:59:11: 6000000 INFO @ Fri, 26 Jun 2020 07:59:11: 2000000 INFO @ Fri, 26 Jun 2020 07:59:17: 11000000 INFO @ Fri, 26 Jun 2020 07:59:19: 7000000 INFO @ Fri, 26 Jun 2020 07:59:19: 3000000 INFO @ Fri, 26 Jun 2020 07:59:25: 12000000 INFO @ Fri, 26 Jun 2020 07:59:27: 8000000 INFO @ Fri, 26 Jun 2020 07:59:27: 4000000 INFO @ Fri, 26 Jun 2020 07:59:33: 13000000 INFO @ Fri, 26 Jun 2020 07:59:34: 9000000 INFO @ Fri, 26 Jun 2020 07:59:35: 5000000 INFO @ Fri, 26 Jun 2020 07:59:41: 14000000 INFO @ Fri, 26 Jun 2020 07:59:42: 10000000 INFO @ Fri, 26 Jun 2020 07:59:43: 6000000 INFO @ Fri, 26 Jun 2020 07:59:49: 15000000 INFO @ Fri, 26 Jun 2020 07:59:50: 11000000 INFO @ Fri, 26 Jun 2020 07:59:51: 7000000 INFO @ Fri, 26 Jun 2020 07:59:57: 16000000 INFO @ Fri, 26 Jun 2020 07:59:58: 12000000 INFO @ Fri, 26 Jun 2020 07:59:59: 8000000 INFO @ Fri, 26 Jun 2020 08:00:04: 17000000 INFO @ Fri, 26 Jun 2020 08:00:06: 13000000 INFO @ Fri, 26 Jun 2020 08:00:07: 9000000 INFO @ Fri, 26 Jun 2020 08:00:12: 18000000 INFO @ Fri, 26 Jun 2020 08:00:14: 14000000 INFO @ Fri, 26 Jun 2020 08:00:15: 10000000 INFO @ Fri, 26 Jun 2020 08:00:20: 19000000 INFO @ Fri, 26 Jun 2020 08:00:22: 15000000 INFO @ Fri, 26 Jun 2020 08:00:23: 11000000 INFO @ Fri, 26 Jun 2020 08:00:27: 20000000 INFO @ Fri, 26 Jun 2020 08:00:29: 16000000 INFO @ Fri, 26 Jun 2020 08:00:31: 12000000 INFO @ Fri, 26 Jun 2020 08:00:35: 21000000 INFO @ Fri, 26 Jun 2020 08:00:38: 17000000 INFO @ Fri, 26 Jun 2020 08:00:39: 13000000 INFO @ Fri, 26 Jun 2020 08:00:43: 22000000 INFO @ Fri, 26 Jun 2020 08:00:45: 18000000 INFO @ Fri, 26 Jun 2020 08:00:47: 14000000 INFO @ Fri, 26 Jun 2020 08:00:50: 23000000 INFO @ Fri, 26 Jun 2020 08:00:53: 19000000 INFO @ Fri, 26 Jun 2020 08:00:55: 15000000 INFO @ Fri, 26 Jun 2020 08:00:58: 24000000 INFO @ Fri, 26 Jun 2020 08:01:01: 20000000 INFO @ Fri, 26 Jun 2020 08:01:02: 16000000 INFO @ Fri, 26 Jun 2020 08:01:05: 25000000 INFO @ Fri, 26 Jun 2020 08:01:09: 21000000 INFO @ Fri, 26 Jun 2020 08:01:10: 17000000 INFO @ Fri, 26 Jun 2020 08:01:12: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 08:01:12: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 08:01:12: #1 total tags in treatment: 11613297 INFO @ Fri, 26 Jun 2020 08:01:12: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:01:12: #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 08:01:12: #1 tags after filtering in treatment: 10315262 INFO @ Fri, 26 Jun 2020 08:01:12: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 26 Jun 2020 08:01:12: #1 finished! INFO @ Fri, 26 Jun 2020 08:01:12: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:01:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:01:13: #2 number of paired peaks: 1860 INFO @ Fri, 26 Jun 2020 08:01:13: start model_add_line... INFO @ Fri, 26 Jun 2020 08:01:13: start X-correlation... INFO @ Fri, 26 Jun 2020 08:01:13: end of X-cor INFO @ Fri, 26 Jun 2020 08:01:13: #2 finished! INFO @ Fri, 26 Jun 2020 08:01:13: #2 predicted fragment length is 175 bps INFO @ Fri, 26 Jun 2020 08:01:13: #2 alternative fragment length(s) may be 4,175 bps INFO @ Fri, 26 Jun 2020 08:01:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2011722/SRX2011722.05_model.r WARNING @ Fri, 26 Jun 2020 08:01:13: #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 08:01:13: #2 You may need to consider one of the other alternative d(s): 4,175 WARNING @ Fri, 26 Jun 2020 08:01:13: #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 08:01:13: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:01:13: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:01:16: 22000000 INFO @ Fri, 26 Jun 2020 08:01:17: 18000000 INFO @ Fri, 26 Jun 2020 08:01:24: 23000000 INFO @ Fri, 26 Jun 2020 08:01:25: 19000000 INFO @ Fri, 26 Jun 2020 08:01:31: 24000000 INFO @ Fri, 26 Jun 2020 08:01:32: 20000000 INFO @ Fri, 26 Jun 2020 08:01:38: 25000000 INFO @ Fri, 26 Jun 2020 08:01:40: 21000000 INFO @ Fri, 26 Jun 2020 08:01:44: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:01:45: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 08:01:45: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 08:01:45: #1 total tags in treatment: 11613297 INFO @ Fri, 26 Jun 2020 08:01:45: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:01:45: #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 08:01:45: #1 tags after filtering in treatment: 10315262 INFO @ Fri, 26 Jun 2020 08:01:45: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 26 Jun 2020 08:01:45: #1 finished! INFO @ Fri, 26 Jun 2020 08:01:45: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:01:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:01:46: #2 number of paired peaks: 1860 INFO @ Fri, 26 Jun 2020 08:01:46: start model_add_line... INFO @ Fri, 26 Jun 2020 08:01:46: start X-correlation... INFO @ Fri, 26 Jun 2020 08:01:46: end of X-cor INFO @ Fri, 26 Jun 2020 08:01:46: #2 finished! INFO @ Fri, 26 Jun 2020 08:01:46: #2 predicted fragment length is 175 bps INFO @ Fri, 26 Jun 2020 08:01:46: #2 alternative fragment length(s) may be 4,175 bps INFO @ Fri, 26 Jun 2020 08:01:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2011722/SRX2011722.10_model.r WARNING @ Fri, 26 Jun 2020 08:01:46: #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 08:01:46: #2 You may need to consider one of the other alternative d(s): 4,175 WARNING @ Fri, 26 Jun 2020 08:01:46: #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 08:01:46: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:01:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:01:47: 22000000 INFO @ Fri, 26 Jun 2020 08:01:54: 23000000 INFO @ Fri, 26 Jun 2020 08:01:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2011722/SRX2011722.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:01:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2011722/SRX2011722.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:01:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2011722/SRX2011722.05_summits.bed INFO @ Fri, 26 Jun 2020 08:01:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4759 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:02:01: 24000000 INFO @ Fri, 26 Jun 2020 08:02:08: 25000000 INFO @ Fri, 26 Jun 2020 08:02:14: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 08:02:14: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 08:02:14: #1 total tags in treatment: 11613297 INFO @ Fri, 26 Jun 2020 08:02:14: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:02:14: #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 08:02:14: #1 tags after filtering in treatment: 10315262 INFO @ Fri, 26 Jun 2020 08:02:14: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 26 Jun 2020 08:02:14: #1 finished! INFO @ Fri, 26 Jun 2020 08:02:14: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:02:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:02:15: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:02:15: #2 number of paired peaks: 1860 INFO @ Fri, 26 Jun 2020 08:02:15: start model_add_line... INFO @ Fri, 26 Jun 2020 08:02:15: start X-correlation... INFO @ Fri, 26 Jun 2020 08:02:15: end of X-cor INFO @ Fri, 26 Jun 2020 08:02:15: #2 finished! INFO @ Fri, 26 Jun 2020 08:02:15: #2 predicted fragment length is 175 bps INFO @ Fri, 26 Jun 2020 08:02:15: #2 alternative fragment length(s) may be 4,175 bps INFO @ Fri, 26 Jun 2020 08:02:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2011722/SRX2011722.20_model.r WARNING @ Fri, 26 Jun 2020 08:02:15: #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 08:02:15: #2 You may need to consider one of the other alternative d(s): 4,175 WARNING @ Fri, 26 Jun 2020 08:02:15: #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 08:02:15: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:02:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:02:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2011722/SRX2011722.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:02:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2011722/SRX2011722.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:02:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2011722/SRX2011722.10_summits.bed INFO @ Fri, 26 Jun 2020 08:02:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2813 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:02:44: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:02:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2011722/SRX2011722.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:02:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2011722/SRX2011722.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:02:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2011722/SRX2011722.20_summits.bed INFO @ Fri, 26 Jun 2020 08:02:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1139 records, 4 fields): 205 millis CompletedMACS2peakCalling