Job ID = 8070226 SRX = SRX7217787 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: 00:12:52 6709555 reads; of these: 6709555 (100.00%) were paired; of these: 1675187 (24.97%) aligned concordantly 0 times 4256621 (63.44%) aligned concordantly exactly 1 time 777747 (11.59%) aligned concordantly >1 times ---- 1675187 pairs aligned concordantly 0 times; of these: 526042 (31.40%) aligned discordantly 1 time ---- 1149145 pairs aligned 0 times concordantly or discordantly; of these: 2298290 mates make up the pairs; of these: 2038598 (88.70%) aligned 0 times 139920 (6.09%) aligned exactly 1 time 119772 (5.21%) aligned >1 times 84.81% overall alignment rate Time searching: 00:12:52 Overall time: 00:12:52 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] 738658 / 5521512 = 0.1338 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 13:19:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7217787/SRX7217787.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7217787/SRX7217787.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7217787/SRX7217787.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7217787/SRX7217787.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 13:19:06: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:19:06: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:19:13: 1000000 INFO @ Sat, 08 Aug 2020 13:19:21: 2000000 INFO @ Sat, 08 Aug 2020 13:19:28: 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 13:19:36: 4000000 INFO @ Sat, 08 Aug 2020 13:19:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7217787/SRX7217787.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7217787/SRX7217787.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7217787/SRX7217787.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7217787/SRX7217787.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 13:19:36: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:19:36: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:19:44: 5000000 INFO @ Sat, 08 Aug 2020 13:19:44: 1000000 INFO @ Sat, 08 Aug 2020 13:19:53: 2000000 INFO @ Sat, 08 Aug 2020 13:19:53: 6000000 INFO @ Sat, 08 Aug 2020 13:20:02: 3000000 INFO @ Sat, 08 Aug 2020 13:20:02: 7000000 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 13:20:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7217787/SRX7217787.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7217787/SRX7217787.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7217787/SRX7217787.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7217787/SRX7217787.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 13:20:06: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:20:06: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:20:11: 4000000 INFO @ Sat, 08 Aug 2020 13:20:11: 8000000 INFO @ Sat, 08 Aug 2020 13:20:15: 1000000 INFO @ Sat, 08 Aug 2020 13:20:20: 5000000 INFO @ Sat, 08 Aug 2020 13:20:20: 9000000 INFO @ Sat, 08 Aug 2020 13:20:24: 2000000 INFO @ Sat, 08 Aug 2020 13:20:28: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:20:28: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:20:28: #1 total tags in treatment: 4347994 INFO @ Sat, 08 Aug 2020 13:20:28: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:20:28: #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 13:20:28: #1 tags after filtering in treatment: 4028656 INFO @ Sat, 08 Aug 2020 13:20:28: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Aug 2020 13:20:28: #1 finished! INFO @ Sat, 08 Aug 2020 13:20:28: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:20:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:20:29: #2 number of paired peaks: 445 WARNING @ Sat, 08 Aug 2020 13:20:29: Fewer paired peaks (445) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 445 pairs to build model! INFO @ Sat, 08 Aug 2020 13:20:29: start model_add_line... INFO @ Sat, 08 Aug 2020 13:20:29: start X-correlation... INFO @ Sat, 08 Aug 2020 13:20:29: end of X-cor INFO @ Sat, 08 Aug 2020 13:20:29: #2 finished! INFO @ Sat, 08 Aug 2020 13:20:29: #2 predicted fragment length is 211 bps INFO @ Sat, 08 Aug 2020 13:20:29: #2 alternative fragment length(s) may be 211 bps INFO @ Sat, 08 Aug 2020 13:20:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7217787/SRX7217787.05_model.r WARNING @ Sat, 08 Aug 2020 13:20:29: #2 Since the d (211) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:20:29: #2 You may need to consider one of the other alternative d(s): 211 WARNING @ Sat, 08 Aug 2020 13:20:29: #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 13:20:29: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:20:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:20:29: 6000000 INFO @ Sat, 08 Aug 2020 13:20:33: 3000000 INFO @ Sat, 08 Aug 2020 13:20:38: 7000000 INFO @ Sat, 08 Aug 2020 13:20:38: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:20:42: 4000000 INFO @ Sat, 08 Aug 2020 13:20:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7217787/SRX7217787.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:20:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7217787/SRX7217787.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:20:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7217787/SRX7217787.05_summits.bed INFO @ Sat, 08 Aug 2020 13:20:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (366 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:20:46: 8000000 INFO @ Sat, 08 Aug 2020 13:20:51: 5000000 INFO @ Sat, 08 Aug 2020 13:20:55: 9000000 INFO @ Sat, 08 Aug 2020 13:21:00: 6000000 INFO @ Sat, 08 Aug 2020 13:21:03: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:21:03: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:21:03: #1 total tags in treatment: 4347994 INFO @ Sat, 08 Aug 2020 13:21:03: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:21:03: #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 13:21:03: #1 tags after filtering in treatment: 4028656 INFO @ Sat, 08 Aug 2020 13:21:03: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Aug 2020 13:21:03: #1 finished! INFO @ Sat, 08 Aug 2020 13:21:03: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:21:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:21:04: #2 number of paired peaks: 445 WARNING @ Sat, 08 Aug 2020 13:21:04: Fewer paired peaks (445) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 445 pairs to build model! INFO @ Sat, 08 Aug 2020 13:21:04: start model_add_line... INFO @ Sat, 08 Aug 2020 13:21:04: start X-correlation... INFO @ Sat, 08 Aug 2020 13:21:04: end of X-cor INFO @ Sat, 08 Aug 2020 13:21:04: #2 finished! INFO @ Sat, 08 Aug 2020 13:21:04: #2 predicted fragment length is 211 bps INFO @ Sat, 08 Aug 2020 13:21:04: #2 alternative fragment length(s) may be 211 bps INFO @ Sat, 08 Aug 2020 13:21:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7217787/SRX7217787.10_model.r WARNING @ Sat, 08 Aug 2020 13:21:04: #2 Since the d (211) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:21:04: #2 You may need to consider one of the other alternative d(s): 211 WARNING @ Sat, 08 Aug 2020 13:21:04: #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 13:21:04: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:21:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:21:08: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:21:13: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:21:17: 8000000 INFO @ Sat, 08 Aug 2020 13:21:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7217787/SRX7217787.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:21:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7217787/SRX7217787.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:21:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7217787/SRX7217787.10_summits.bed INFO @ Sat, 08 Aug 2020 13:21:17: 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 13:21:26: 9000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:21:33: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:21:33: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:21:33: #1 total tags in treatment: 4347994 INFO @ Sat, 08 Aug 2020 13:21:33: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:21:33: #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 13:21:33: #1 tags after filtering in treatment: 4028656 INFO @ Sat, 08 Aug 2020 13:21:33: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Aug 2020 13:21:33: #1 finished! INFO @ Sat, 08 Aug 2020 13:21:33: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:21:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:21:34: #2 number of paired peaks: 445 WARNING @ Sat, 08 Aug 2020 13:21:34: Fewer paired peaks (445) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 445 pairs to build model! INFO @ Sat, 08 Aug 2020 13:21:34: start model_add_line... INFO @ Sat, 08 Aug 2020 13:21:34: start X-correlation... INFO @ Sat, 08 Aug 2020 13:21:34: end of X-cor INFO @ Sat, 08 Aug 2020 13:21:34: #2 finished! INFO @ Sat, 08 Aug 2020 13:21:34: #2 predicted fragment length is 211 bps INFO @ Sat, 08 Aug 2020 13:21:34: #2 alternative fragment length(s) may be 211 bps INFO @ Sat, 08 Aug 2020 13:21:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7217787/SRX7217787.20_model.r WARNING @ Sat, 08 Aug 2020 13:21:34: #2 Since the d (211) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:21:34: #2 You may need to consider one of the other alternative d(s): 211 WARNING @ Sat, 08 Aug 2020 13:21:34: #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 13:21:34: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:21:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:21:43: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:21:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7217787/SRX7217787.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:21:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7217787/SRX7217787.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:21:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7217787/SRX7217787.20_summits.bed INFO @ Sat, 08 Aug 2020 13:21:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (167 records, 4 fields): 1 millis CompletedMACS2peakCalling