Job ID = 8069392 SRX = SRX7217788 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 'SRR10533865'... 2020-08-08T03:32:14 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:36:20 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:36:20 prefetch.2.10.7: 1) 'SRR10533865' was downloaded successfully 2020-08-08T03:36:20 prefetch.2.10.7: 'SRR10533865' has 0 unresolved dependencies Read 7412216 spots for SRR10533865/SRR10533865.sra Written 7412216 spots for SRR10533865/SRR10533865.sra fastq に変換しました。 bowtie でマッピング中... Your job 8070433 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:13:40 7412216 reads; of these: 7412216 (100.00%) were paired; of these: 1475136 (19.90%) aligned concordantly 0 times 5067850 (68.37%) aligned concordantly exactly 1 time 869230 (11.73%) aligned concordantly >1 times ---- 1475136 pairs aligned concordantly 0 times; of these: 729806 (49.47%) aligned discordantly 1 time ---- 745330 pairs aligned 0 times concordantly or discordantly; of these: 1490660 mates make up the pairs; of these: 1228853 (82.44%) aligned 0 times 119780 (8.04%) aligned exactly 1 time 142027 (9.53%) aligned >1 times 91.71% overall alignment rate Time searching: 00:13:41 Overall time: 00:13:41 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] 954665 / 6619125 = 0.1442 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 12:56:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217788/SRX7217788.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217788/SRX7217788.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217788/SRX7217788.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217788/SRX7217788.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 12:56:20: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:56:20: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:56:29: 1000000 INFO @ Sat, 08 Aug 2020 12:56:38: 2000000 INFO @ Sat, 08 Aug 2020 12:56:47: 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 12:56:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217788/SRX7217788.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217788/SRX7217788.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217788/SRX7217788.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217788/SRX7217788.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 12:56:50: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:56:50: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:56:56: 4000000 INFO @ Sat, 08 Aug 2020 12:57:00: 1000000 INFO @ Sat, 08 Aug 2020 12:57:06: 5000000 INFO @ Sat, 08 Aug 2020 12:57:11: 2000000 INFO @ Sat, 08 Aug 2020 12:57:16: 6000000 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 12:57:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217788/SRX7217788.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217788/SRX7217788.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217788/SRX7217788.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217788/SRX7217788.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 12:57:20: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:57:20: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:57:21: 3000000 INFO @ Sat, 08 Aug 2020 12:57:26: 7000000 INFO @ Sat, 08 Aug 2020 12:57:30: 1000000 INFO @ Sat, 08 Aug 2020 12:57:31: 4000000 INFO @ Sat, 08 Aug 2020 12:57:36: 8000000 INFO @ Sat, 08 Aug 2020 12:57:41: 2000000 INFO @ Sat, 08 Aug 2020 12:57:41: 5000000 INFO @ Sat, 08 Aug 2020 12:57:46: 9000000 INFO @ Sat, 08 Aug 2020 12:57:51: 3000000 INFO @ Sat, 08 Aug 2020 12:57:52: 6000000 INFO @ Sat, 08 Aug 2020 12:57:57: 10000000 INFO @ Sat, 08 Aug 2020 12:58:01: 4000000 INFO @ Sat, 08 Aug 2020 12:58:02: 7000000 INFO @ Sat, 08 Aug 2020 12:58:07: 11000000 INFO @ Sat, 08 Aug 2020 12:58:12: 5000000 INFO @ Sat, 08 Aug 2020 12:58:13: 8000000 INFO @ Sat, 08 Aug 2020 12:58:15: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:58:15: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:58:15: #1 total tags in treatment: 5064469 INFO @ Sat, 08 Aug 2020 12:58:15: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:58:15: #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 12:58:15: #1 tags after filtering in treatment: 4693970 INFO @ Sat, 08 Aug 2020 12:58:15: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Aug 2020 12:58:15: #1 finished! INFO @ Sat, 08 Aug 2020 12:58:15: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:58:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:58:15: #2 number of paired peaks: 434 WARNING @ Sat, 08 Aug 2020 12:58:15: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Sat, 08 Aug 2020 12:58:15: start model_add_line... INFO @ Sat, 08 Aug 2020 12:58:15: start X-correlation... INFO @ Sat, 08 Aug 2020 12:58:15: end of X-cor INFO @ Sat, 08 Aug 2020 12:58:15: #2 finished! INFO @ Sat, 08 Aug 2020 12:58:15: #2 predicted fragment length is 205 bps INFO @ Sat, 08 Aug 2020 12:58:15: #2 alternative fragment length(s) may be 205 bps INFO @ Sat, 08 Aug 2020 12:58:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217788/SRX7217788.05_model.r WARNING @ Sat, 08 Aug 2020 12:58:15: #2 Since the d (205) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:58:15: #2 You may need to consider one of the other alternative d(s): 205 WARNING @ Sat, 08 Aug 2020 12:58:15: #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 12:58:15: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:58:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:58:23: 6000000 INFO @ Sat, 08 Aug 2020 12:58:23: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 12:58:26: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:58:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217788/SRX7217788.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:58:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217788/SRX7217788.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:58:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217788/SRX7217788.05_summits.bed INFO @ Sat, 08 Aug 2020 12:58:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (341 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:58:33: 7000000 INFO @ Sat, 08 Aug 2020 12:58:33: 10000000 INFO @ Sat, 08 Aug 2020 12:58:43: 11000000 INFO @ Sat, 08 Aug 2020 12:58:43: 8000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:58:49: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:58:49: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:58:49: #1 total tags in treatment: 5064469 INFO @ Sat, 08 Aug 2020 12:58:49: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:58:49: #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 12:58:49: #1 tags after filtering in treatment: 4693970 INFO @ Sat, 08 Aug 2020 12:58:49: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Aug 2020 12:58:49: #1 finished! INFO @ Sat, 08 Aug 2020 12:58:49: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:58:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:58:50: #2 number of paired peaks: 434 WARNING @ Sat, 08 Aug 2020 12:58:50: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Sat, 08 Aug 2020 12:58:50: start model_add_line... INFO @ Sat, 08 Aug 2020 12:58:50: start X-correlation... INFO @ Sat, 08 Aug 2020 12:58:50: end of X-cor INFO @ Sat, 08 Aug 2020 12:58:50: #2 finished! INFO @ Sat, 08 Aug 2020 12:58:50: #2 predicted fragment length is 205 bps INFO @ Sat, 08 Aug 2020 12:58:50: #2 alternative fragment length(s) may be 205 bps INFO @ Sat, 08 Aug 2020 12:58:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217788/SRX7217788.10_model.r WARNING @ Sat, 08 Aug 2020 12:58:50: #2 Since the d (205) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:58:50: #2 You may need to consider one of the other alternative d(s): 205 WARNING @ Sat, 08 Aug 2020 12:58:50: #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 12:58:50: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:58:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:58:53: 9000000 INFO @ Sat, 08 Aug 2020 12:59:00: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:59:02: 10000000 INFO @ Sat, 08 Aug 2020 12:59:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217788/SRX7217788.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:59:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217788/SRX7217788.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:59:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217788/SRX7217788.10_summits.bed INFO @ Sat, 08 Aug 2020 12:59:05: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (241 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:59:11: 11000000 INFO @ Sat, 08 Aug 2020 12:59:18: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:59:18: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:59:18: #1 total tags in treatment: 5064469 INFO @ Sat, 08 Aug 2020 12:59:18: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:59:18: #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 12:59:18: #1 tags after filtering in treatment: 4693970 INFO @ Sat, 08 Aug 2020 12:59:18: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Aug 2020 12:59:18: #1 finished! INFO @ Sat, 08 Aug 2020 12:59:18: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:59:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:59:18: #2 number of paired peaks: 434 WARNING @ Sat, 08 Aug 2020 12:59:18: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Sat, 08 Aug 2020 12:59:18: start model_add_line... INFO @ Sat, 08 Aug 2020 12:59:18: start X-correlation... INFO @ Sat, 08 Aug 2020 12:59:18: end of X-cor INFO @ Sat, 08 Aug 2020 12:59:18: #2 finished! INFO @ Sat, 08 Aug 2020 12:59:18: #2 predicted fragment length is 205 bps INFO @ Sat, 08 Aug 2020 12:59:18: #2 alternative fragment length(s) may be 205 bps INFO @ Sat, 08 Aug 2020 12:59:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217788/SRX7217788.20_model.r WARNING @ Sat, 08 Aug 2020 12:59:18: #2 Since the d (205) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:59:18: #2 You may need to consider one of the other alternative d(s): 205 WARNING @ Sat, 08 Aug 2020 12:59:18: #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 12:59:18: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:59:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:59:29: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:59:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217788/SRX7217788.20_peaks.xls INFO @ Sat, 08 Aug 2020 12:59:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217788/SRX7217788.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:59:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217788/SRX7217788.20_summits.bed INFO @ Sat, 08 Aug 2020 12:59:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (176 records, 4 fields): 1 millis CompletedMACS2peakCalling