Job ID = 8069469 SRX = SRX8392432 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:33:11 prefetch.2.10.7: 1) Downloading 'SRR11842085'... 2020-08-08T03:33:11 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:35:10 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:35:10 prefetch.2.10.7: 1) 'SRR11842085' was downloaded successfully 2020-08-08T03:35:10 prefetch.2.10.7: 'SRR11842085' has 0 unresolved dependencies Read 7913909 spots for SRR11842085/SRR11842085.sra Written 7913909 spots for SRR11842085/SRR11842085.sra fastq に変換しました。 bowtie でマッピング中... Your job 8070268 ("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: 00:11:31 7913909 reads; of these: 7913909 (100.00%) were paired; of these: 3508393 (44.33%) aligned concordantly 0 times 3862348 (48.80%) aligned concordantly exactly 1 time 543168 (6.86%) aligned concordantly >1 times ---- 3508393 pairs aligned concordantly 0 times; of these: 1005222 (28.65%) aligned discordantly 1 time ---- 2503171 pairs aligned 0 times concordantly or discordantly; of these: 5006342 mates make up the pairs; of these: 4703761 (93.96%) aligned 0 times 127174 (2.54%) aligned exactly 1 time 175407 (3.50%) aligned >1 times 70.28% overall alignment rate Time searching: 00:11:31 Overall time: 00:11:31 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] 1131346 / 5366001 = 0.2108 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 12:52:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392432/SRX8392432.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392432/SRX8392432.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392432/SRX8392432.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392432/SRX8392432.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 12:52:28: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:52:28: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:52:35: 1000000 INFO @ Sat, 08 Aug 2020 12:52:41: 2000000 INFO @ Sat, 08 Aug 2020 12:52:48: 3000000 INFO @ Sat, 08 Aug 2020 12:52:55: 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 @ Sat, 08 Aug 2020 12:52:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392432/SRX8392432.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392432/SRX8392432.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392432/SRX8392432.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392432/SRX8392432.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 12:52:58: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:52:58: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:53:01: 5000000 INFO @ Sat, 08 Aug 2020 12:53:05: 1000000 INFO @ Sat, 08 Aug 2020 12:53:09: 6000000 INFO @ Sat, 08 Aug 2020 12:53:13: 2000000 INFO @ Sat, 08 Aug 2020 12:53:16: 7000000 INFO @ Sat, 08 Aug 2020 12:53:20: 3000000 INFO @ Sat, 08 Aug 2020 12:53:23: 8000000 BedGraph に変換中... INFO @ Sat, 08 Aug 2020 12:53:27: 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 @ Sat, 08 Aug 2020 12:53:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392432/SRX8392432.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392432/SRX8392432.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392432/SRX8392432.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392432/SRX8392432.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 12:53:28: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:53:28: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:53:29: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:53:29: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:53:29: #1 total tags in treatment: 3437175 INFO @ Sat, 08 Aug 2020 12:53:29: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:53:29: #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 12:53:29: #1 tags after filtering in treatment: 3046556 INFO @ Sat, 08 Aug 2020 12:53:29: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 08 Aug 2020 12:53:29: #1 finished! INFO @ Sat, 08 Aug 2020 12:53:29: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:53:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:53:29: #2 number of paired peaks: 2819 INFO @ Sat, 08 Aug 2020 12:53:29: start model_add_line... INFO @ Sat, 08 Aug 2020 12:53:29: start X-correlation... INFO @ Sat, 08 Aug 2020 12:53:29: end of X-cor INFO @ Sat, 08 Aug 2020 12:53:29: #2 finished! INFO @ Sat, 08 Aug 2020 12:53:29: #2 predicted fragment length is 201 bps INFO @ Sat, 08 Aug 2020 12:53:29: #2 alternative fragment length(s) may be 201 bps INFO @ Sat, 08 Aug 2020 12:53:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392432/SRX8392432.05_model.r WARNING @ Sat, 08 Aug 2020 12:53:29: #2 Since the d (201) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:53:29: #2 You may need to consider one of the other alternative d(s): 201 WARNING @ Sat, 08 Aug 2020 12:53:29: #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 12:53:29: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:53:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:53:34: 5000000 INFO @ Sat, 08 Aug 2020 12:53:35: 1000000 INFO @ Sat, 08 Aug 2020 12:53:37: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:53:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392432/SRX8392432.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:53:41: 6000000 INFO @ Sat, 08 Aug 2020 12:53:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392432/SRX8392432.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:53:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392432/SRX8392432.05_summits.bed INFO @ Sat, 08 Aug 2020 12:53:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5917 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:53:43: 2000000 INFO @ Sat, 08 Aug 2020 12:53:48: 7000000 INFO @ Sat, 08 Aug 2020 12:53:50: 3000000 INFO @ Sat, 08 Aug 2020 12:53:55: 8000000 INFO @ Sat, 08 Aug 2020 12:53:57: 4000000 INFO @ Sat, 08 Aug 2020 12:54:01: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:54:01: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:54:01: #1 total tags in treatment: 3437175 INFO @ Sat, 08 Aug 2020 12:54:01: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:54:01: #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 12:54:01: #1 tags after filtering in treatment: 3046556 INFO @ Sat, 08 Aug 2020 12:54:01: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 08 Aug 2020 12:54:01: #1 finished! INFO @ Sat, 08 Aug 2020 12:54:01: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:54:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:54:01: #2 number of paired peaks: 2819 INFO @ Sat, 08 Aug 2020 12:54:01: start model_add_line... INFO @ Sat, 08 Aug 2020 12:54:01: start X-correlation... INFO @ Sat, 08 Aug 2020 12:54:01: end of X-cor INFO @ Sat, 08 Aug 2020 12:54:01: #2 finished! INFO @ Sat, 08 Aug 2020 12:54:01: #2 predicted fragment length is 201 bps INFO @ Sat, 08 Aug 2020 12:54:01: #2 alternative fragment length(s) may be 201 bps INFO @ Sat, 08 Aug 2020 12:54:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392432/SRX8392432.10_model.r WARNING @ Sat, 08 Aug 2020 12:54:01: #2 Since the d (201) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:54:01: #2 You may need to consider one of the other alternative d(s): 201 WARNING @ Sat, 08 Aug 2020 12:54:01: #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 12:54:01: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:54:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:54:04: 5000000 INFO @ Sat, 08 Aug 2020 12:54:09: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:54:10: 6000000 INFO @ Sat, 08 Aug 2020 12:54:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392432/SRX8392432.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:54:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392432/SRX8392432.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:54:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392432/SRX8392432.10_summits.bed INFO @ Sat, 08 Aug 2020 12:54:12: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (3462 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 12:54:17: 7000000 INFO @ Sat, 08 Aug 2020 12:54:24: 8000000 INFO @ Sat, 08 Aug 2020 12:54:30: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:54:30: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:54:30: #1 total tags in treatment: 3437175 INFO @ Sat, 08 Aug 2020 12:54:30: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:54:30: #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 12:54:30: #1 tags after filtering in treatment: 3046556 INFO @ Sat, 08 Aug 2020 12:54:30: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 08 Aug 2020 12:54:30: #1 finished! INFO @ Sat, 08 Aug 2020 12:54:30: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:54:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:54:30: #2 number of paired peaks: 2819 INFO @ Sat, 08 Aug 2020 12:54:30: start model_add_line... INFO @ Sat, 08 Aug 2020 12:54:30: start X-correlation... INFO @ Sat, 08 Aug 2020 12:54:30: end of X-cor INFO @ Sat, 08 Aug 2020 12:54:30: #2 finished! INFO @ Sat, 08 Aug 2020 12:54:30: #2 predicted fragment length is 201 bps INFO @ Sat, 08 Aug 2020 12:54:30: #2 alternative fragment length(s) may be 201 bps INFO @ Sat, 08 Aug 2020 12:54:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392432/SRX8392432.20_model.r WARNING @ Sat, 08 Aug 2020 12:54:30: #2 Since the d (201) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:54:30: #2 You may need to consider one of the other alternative d(s): 201 WARNING @ Sat, 08 Aug 2020 12:54:30: #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 12:54:30: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:54:30: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:54:38: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:54:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392432/SRX8392432.20_peaks.xls INFO @ Sat, 08 Aug 2020 12:54:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392432/SRX8392432.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:54:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392432/SRX8392432.20_summits.bed INFO @ Sat, 08 Aug 2020 12:54:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1894 records, 4 fields): 3 millis CompletedMACS2peakCalling