Job ID = 8069401 SRX = SRX7217791 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:32:14 prefetch.2.10.7: 1) Downloading 'SRR10533868'... 2020-08-08T03:32:14 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:37:25 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:37:25 prefetch.2.10.7: 1) 'SRR10533868' was downloaded successfully 2020-08-08T03:37:25 prefetch.2.10.7: 'SRR10533868' has 0 unresolved dependencies Read 7395069 spots for SRR10533868/SRR10533868.sra Written 7395069 spots for SRR10533868/SRR10533868.sra fastq に変換しました。 bowtie でマッピング中... Your job 8070461 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:13:10 7395069 reads; of these: 7395069 (100.00%) were paired; of these: 807281 (10.92%) aligned concordantly 0 times 5780938 (78.17%) aligned concordantly exactly 1 time 806850 (10.91%) aligned concordantly >1 times ---- 807281 pairs aligned concordantly 0 times; of these: 290095 (35.93%) aligned discordantly 1 time ---- 517186 pairs aligned 0 times concordantly or discordantly; of these: 1034372 mates make up the pairs; of these: 851455 (82.32%) aligned 0 times 99638 (9.63%) aligned exactly 1 time 83279 (8.05%) aligned >1 times 94.24% overall alignment rate Time searching: 00:13:10 Overall time: 00:13:10 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 12 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] 2614458 / 6854490 = 0.3814 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 @ Sat, 08 Aug 2020 12:56:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217791/SRX7217791.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217791/SRX7217791.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217791/SRX7217791.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217791/SRX7217791.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 @ Sat, 08 Aug 2020 12:56:32: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:56:32: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:56:41: 1000000 INFO @ Sat, 08 Aug 2020 12:56:49: 2000000 INFO @ Sat, 08 Aug 2020 12:56:58: 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 @ Sat, 08 Aug 2020 12:57:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217791/SRX7217791.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217791/SRX7217791.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217791/SRX7217791.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217791/SRX7217791.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 @ Sat, 08 Aug 2020 12:57:02: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:57:02: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:57:06: 4000000 INFO @ Sat, 08 Aug 2020 12:57:11: 1000000 INFO @ Sat, 08 Aug 2020 12:57:15: 5000000 INFO @ Sat, 08 Aug 2020 12:57:20: 2000000 INFO @ Sat, 08 Aug 2020 12:57:24: 6000000 INFO @ Sat, 08 Aug 2020 12:57:29: 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 @ Sat, 08 Aug 2020 12:57:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217791/SRX7217791.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217791/SRX7217791.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217791/SRX7217791.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217791/SRX7217791.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 @ Sat, 08 Aug 2020 12:57:32: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:57:32: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:57:33: 7000000 INFO @ Sat, 08 Aug 2020 12:57:37: 4000000 INFO @ Sat, 08 Aug 2020 12:57:41: 1000000 INFO @ Sat, 08 Aug 2020 12:57:42: 8000000 INFO @ Sat, 08 Aug 2020 12:57:46: 5000000 INFO @ Sat, 08 Aug 2020 12:57:48: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:57:48: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:57:48: #1 total tags in treatment: 4020909 INFO @ Sat, 08 Aug 2020 12:57:48: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:57:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:57:48: #1 tags after filtering in treatment: 3615855 INFO @ Sat, 08 Aug 2020 12:57:48: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 12:57:48: #1 finished! INFO @ Sat, 08 Aug 2020 12:57:48: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:57:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:57:48: #2 number of paired peaks: 1756 INFO @ Sat, 08 Aug 2020 12:57:48: start model_add_line... INFO @ Sat, 08 Aug 2020 12:57:48: start X-correlation... INFO @ Sat, 08 Aug 2020 12:57:48: end of X-cor INFO @ Sat, 08 Aug 2020 12:57:48: #2 finished! INFO @ Sat, 08 Aug 2020 12:57:48: #2 predicted fragment length is 219 bps INFO @ Sat, 08 Aug 2020 12:57:48: #2 alternative fragment length(s) may be 219 bps INFO @ Sat, 08 Aug 2020 12:57:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217791/SRX7217791.05_model.r WARNING @ Sat, 08 Aug 2020 12:57:48: #2 Since the d (219) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:57:48: #2 You may need to consider one of the other alternative d(s): 219 WARNING @ Sat, 08 Aug 2020 12:57:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 12:57:48: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:57:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:57:50: 2000000 INFO @ Sat, 08 Aug 2020 12:57:55: 6000000 INFO @ Sat, 08 Aug 2020 12:57:58: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:57:59: 3000000 INFO @ Sat, 08 Aug 2020 12:58:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217791/SRX7217791.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:58:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217791/SRX7217791.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:58:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217791/SRX7217791.05_summits.bed INFO @ Sat, 08 Aug 2020 12:58:02: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4572 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:58:05: 7000000 INFO @ Sat, 08 Aug 2020 12:58:07: 4000000 INFO @ Sat, 08 Aug 2020 12:58:14: 8000000 INFO @ Sat, 08 Aug 2020 12:58:16: 5000000 INFO @ Sat, 08 Aug 2020 12:58:20: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:58:20: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:58:20: #1 total tags in treatment: 4020909 INFO @ Sat, 08 Aug 2020 12:58:20: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:58:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:58:20: #1 tags after filtering in treatment: 3615855 INFO @ Sat, 08 Aug 2020 12:58:20: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 12:58:20: #1 finished! INFO @ Sat, 08 Aug 2020 12:58:20: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:58:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:58:20: #2 number of paired peaks: 1756 INFO @ Sat, 08 Aug 2020 12:58:20: start model_add_line... INFO @ Sat, 08 Aug 2020 12:58:21: start X-correlation... INFO @ Sat, 08 Aug 2020 12:58:21: end of X-cor INFO @ Sat, 08 Aug 2020 12:58:21: #2 finished! INFO @ Sat, 08 Aug 2020 12:58:21: #2 predicted fragment length is 219 bps INFO @ Sat, 08 Aug 2020 12:58:21: #2 alternative fragment length(s) may be 219 bps INFO @ Sat, 08 Aug 2020 12:58:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217791/SRX7217791.10_model.r WARNING @ Sat, 08 Aug 2020 12:58:21: #2 Since the d (219) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:58:21: #2 You may need to consider one of the other alternative d(s): 219 WARNING @ Sat, 08 Aug 2020 12:58:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 12:58:21: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:58:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:58:24: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 12:58:30: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:58:32: 7000000 INFO @ Sat, 08 Aug 2020 12:58:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217791/SRX7217791.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:58:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217791/SRX7217791.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:58:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217791/SRX7217791.10_summits.bed INFO @ Sat, 08 Aug 2020 12:58:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2321 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:58:41: 8000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:58:46: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:58:46: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:58:46: #1 total tags in treatment: 4020909 INFO @ Sat, 08 Aug 2020 12:58:46: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:58:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:58:47: #1 tags after filtering in treatment: 3615855 INFO @ Sat, 08 Aug 2020 12:58:47: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 12:58:47: #1 finished! INFO @ Sat, 08 Aug 2020 12:58:47: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:58:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:58:47: #2 number of paired peaks: 1756 INFO @ Sat, 08 Aug 2020 12:58:47: start model_add_line... INFO @ Sat, 08 Aug 2020 12:58:47: start X-correlation... INFO @ Sat, 08 Aug 2020 12:58:47: end of X-cor INFO @ Sat, 08 Aug 2020 12:58:47: #2 finished! INFO @ Sat, 08 Aug 2020 12:58:47: #2 predicted fragment length is 219 bps INFO @ Sat, 08 Aug 2020 12:58:47: #2 alternative fragment length(s) may be 219 bps INFO @ Sat, 08 Aug 2020 12:58:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217791/SRX7217791.20_model.r WARNING @ Sat, 08 Aug 2020 12:58:47: #2 Since the d (219) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:58:47: #2 You may need to consider one of the other alternative d(s): 219 WARNING @ Sat, 08 Aug 2020 12:58:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 12:58:47: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:58:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:58:56: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:59:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217791/SRX7217791.20_peaks.xls INFO @ Sat, 08 Aug 2020 12:59:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217791/SRX7217791.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:59:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217791/SRX7217791.20_summits.bed INFO @ Sat, 08 Aug 2020 12:59:00: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (893 records, 4 fields): 3 millis CompletedMACS2peakCalling