Job ID = 8070296 SRX = SRX7217779 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 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: 00:12:18 7842201 reads; of these: 7842201 (100.00%) were paired; of these: 3445789 (43.94%) aligned concordantly 0 times 3700940 (47.19%) aligned concordantly exactly 1 time 695472 (8.87%) aligned concordantly >1 times ---- 3445789 pairs aligned concordantly 0 times; of these: 707841 (20.54%) aligned discordantly 1 time ---- 2737948 pairs aligned 0 times concordantly or discordantly; of these: 5475896 mates make up the pairs; of these: 5133633 (93.75%) aligned 0 times 195540 (3.57%) aligned exactly 1 time 146723 (2.68%) aligned >1 times 67.27% overall alignment rate Time searching: 00:12:18 Overall time: 00:12:18 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 8 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] 745836 / 5056431 = 0.1475 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 13:18:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7217779/SRX7217779.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7217779/SRX7217779.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7217779/SRX7217779.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7217779/SRX7217779.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 13:18:48: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:18:48: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:18:56: 1000000 INFO @ Sat, 08 Aug 2020 13:19:03: 2000000 INFO @ Sat, 08 Aug 2020 13:19:10: 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 13:19:18: 4000000 INFO @ Sat, 08 Aug 2020 13:19:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7217779/SRX7217779.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7217779/SRX7217779.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7217779/SRX7217779.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7217779/SRX7217779.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 13:19:18: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:19:18: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:19:25: 1000000 INFO @ Sat, 08 Aug 2020 13:19:25: 5000000 INFO @ Sat, 08 Aug 2020 13:19:31: 2000000 INFO @ Sat, 08 Aug 2020 13:19:33: 6000000 INFO @ Sat, 08 Aug 2020 13:19:37: 3000000 INFO @ Sat, 08 Aug 2020 13:19:40: 7000000 INFO @ Sat, 08 Aug 2020 13:19:44: 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 @ Sat, 08 Aug 2020 13:19:48: 8000000 INFO @ Sat, 08 Aug 2020 13:19:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7217779/SRX7217779.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7217779/SRX7217779.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7217779/SRX7217779.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7217779/SRX7217779.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 13:19:48: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:19:48: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:19:50: 5000000 INFO @ Sat, 08 Aug 2020 13:19:55: 9000000 INFO @ Sat, 08 Aug 2020 13:19:55: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:19:55: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:19:55: #1 total tags in treatment: 3730303 INFO @ Sat, 08 Aug 2020 13:19:55: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:19:55: #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 13:19:56: #1 tags after filtering in treatment: 3419863 INFO @ Sat, 08 Aug 2020 13:19:56: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 13:19:56: #1 finished! INFO @ Sat, 08 Aug 2020 13:19:56: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:19:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:19:56: #2 number of paired peaks: 494 WARNING @ Sat, 08 Aug 2020 13:19:56: Fewer paired peaks (494) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 494 pairs to build model! INFO @ Sat, 08 Aug 2020 13:19:56: start model_add_line... INFO @ Sat, 08 Aug 2020 13:19:56: 1000000 INFO @ Sat, 08 Aug 2020 13:19:56: start X-correlation... INFO @ Sat, 08 Aug 2020 13:19:56: end of X-cor INFO @ Sat, 08 Aug 2020 13:19:56: #2 finished! INFO @ Sat, 08 Aug 2020 13:19:56: #2 predicted fragment length is 202 bps INFO @ Sat, 08 Aug 2020 13:19:56: #2 alternative fragment length(s) may be 202 bps INFO @ Sat, 08 Aug 2020 13:19:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7217779/SRX7217779.05_model.r WARNING @ Sat, 08 Aug 2020 13:19:56: #2 Since the d (202) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:19:56: #2 You may need to consider one of the other alternative d(s): 202 WARNING @ Sat, 08 Aug 2020 13:19:56: #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 13:19:56: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:19:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:19:57: 6000000 INFO @ Sat, 08 Aug 2020 13:20:03: 7000000 INFO @ Sat, 08 Aug 2020 13:20:03: 2000000 INFO @ Sat, 08 Aug 2020 13:20:04: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:20:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7217779/SRX7217779.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:20:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7217779/SRX7217779.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:20:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7217779/SRX7217779.05_summits.bed INFO @ Sat, 08 Aug 2020 13:20:08: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (391 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:20:09: 8000000 INFO @ Sat, 08 Aug 2020 13:20:11: 3000000 INFO @ Sat, 08 Aug 2020 13:20:16: 9000000 INFO @ Sat, 08 Aug 2020 13:20:16: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:20:16: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:20:16: #1 total tags in treatment: 3730303 INFO @ Sat, 08 Aug 2020 13:20:16: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:20:16: #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 13:20:16: #1 tags after filtering in treatment: 3419863 INFO @ Sat, 08 Aug 2020 13:20:16: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 13:20:16: #1 finished! INFO @ Sat, 08 Aug 2020 13:20:16: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:20:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:20:16: #2 number of paired peaks: 494 WARNING @ Sat, 08 Aug 2020 13:20:16: Fewer paired peaks (494) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 494 pairs to build model! INFO @ Sat, 08 Aug 2020 13:20:16: start model_add_line... INFO @ Sat, 08 Aug 2020 13:20:16: start X-correlation... INFO @ Sat, 08 Aug 2020 13:20:16: end of X-cor INFO @ Sat, 08 Aug 2020 13:20:16: #2 finished! INFO @ Sat, 08 Aug 2020 13:20:16: #2 predicted fragment length is 202 bps INFO @ Sat, 08 Aug 2020 13:20:16: #2 alternative fragment length(s) may be 202 bps INFO @ Sat, 08 Aug 2020 13:20:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7217779/SRX7217779.10_model.r WARNING @ Sat, 08 Aug 2020 13:20:16: #2 Since the d (202) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:20:16: #2 You may need to consider one of the other alternative d(s): 202 WARNING @ Sat, 08 Aug 2020 13:20:16: #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 13:20:16: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:20:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:20:19: 4000000 INFO @ Sat, 08 Aug 2020 13:20:24: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:20:26: 5000000 INFO @ Sat, 08 Aug 2020 13:20:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7217779/SRX7217779.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:20:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7217779/SRX7217779.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:20:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7217779/SRX7217779.10_summits.bed INFO @ Sat, 08 Aug 2020 13:20:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (260 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:20:34: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:20:42: 7000000 INFO @ Sat, 08 Aug 2020 13:20:49: 8000000 INFO @ Sat, 08 Aug 2020 13:20:57: 9000000 INFO @ Sat, 08 Aug 2020 13:20:57: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:20:57: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:20:57: #1 total tags in treatment: 3730303 INFO @ Sat, 08 Aug 2020 13:20:57: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:20:57: #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 13:20:57: #1 tags after filtering in treatment: 3419863 INFO @ Sat, 08 Aug 2020 13:20:57: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 13:20:57: #1 finished! INFO @ Sat, 08 Aug 2020 13:20:57: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:20:57: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:20:58: #2 number of paired peaks: 494 WARNING @ Sat, 08 Aug 2020 13:20:58: Fewer paired peaks (494) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 494 pairs to build model! INFO @ Sat, 08 Aug 2020 13:20:58: start model_add_line... INFO @ Sat, 08 Aug 2020 13:20:58: start X-correlation... INFO @ Sat, 08 Aug 2020 13:20:58: end of X-cor INFO @ Sat, 08 Aug 2020 13:20:58: #2 finished! INFO @ Sat, 08 Aug 2020 13:20:58: #2 predicted fragment length is 202 bps INFO @ Sat, 08 Aug 2020 13:20:58: #2 alternative fragment length(s) may be 202 bps INFO @ Sat, 08 Aug 2020 13:20:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7217779/SRX7217779.20_model.r WARNING @ Sat, 08 Aug 2020 13:20:58: #2 Since the d (202) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:20:58: #2 You may need to consider one of the other alternative d(s): 202 WARNING @ Sat, 08 Aug 2020 13:20:58: #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 13:20:58: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:20:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:21:06: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:21:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7217779/SRX7217779.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:21:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7217779/SRX7217779.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:21:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7217779/SRX7217779.20_summits.bed INFO @ Sat, 08 Aug 2020 13:21:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (174 records, 4 fields): 1 millis CompletedMACS2peakCalling