Job ID = 8069444 SRX = SRX8392424 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:32:44 prefetch.2.10.7: 1) Downloading 'SRR11842077'... 2020-08-08T03:32:44 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:35:19 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:35:19 prefetch.2.10.7: 1) 'SRR11842077' was downloaded successfully 2020-08-08T03:35:19 prefetch.2.10.7: 'SRR11842077' has 0 unresolved dependencies Read 10299312 spots for SRR11842077/SRR11842077.sra Written 10299312 spots for SRR11842077/SRR11842077.sra fastq に変換しました。 bowtie でマッピング中... Your job 8070519 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:16:03 10299312 reads; of these: 10299312 (100.00%) were paired; of these: 4466440 (43.37%) aligned concordantly 0 times 4922796 (47.80%) aligned concordantly exactly 1 time 910076 (8.84%) aligned concordantly >1 times ---- 4466440 pairs aligned concordantly 0 times; of these: 1212808 (27.15%) aligned discordantly 1 time ---- 3253632 pairs aligned 0 times concordantly or discordantly; of these: 6507264 mates make up the pairs; of these: 6071798 (93.31%) aligned 0 times 201066 (3.09%) aligned exactly 1 time 234400 (3.60%) aligned >1 times 70.52% overall alignment rate Time searching: 00:16:04 Overall time: 00:16:04 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] 1435481 / 6979614 = 0.2057 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 12:58:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392424/SRX8392424.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392424/SRX8392424.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392424/SRX8392424.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392424/SRX8392424.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 12:58:45: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:58:45: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:58:55: 1000000 INFO @ Sat, 08 Aug 2020 12:59:05: 2000000 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 12:59:15: 3000000 INFO @ Sat, 08 Aug 2020 12:59:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392424/SRX8392424.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392424/SRX8392424.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392424/SRX8392424.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392424/SRX8392424.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 12:59:15: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:59:15: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:59:26: 4000000 INFO @ Sat, 08 Aug 2020 12:59:26: 1000000 INFO @ Sat, 08 Aug 2020 12:59:38: 5000000 INFO @ Sat, 08 Aug 2020 12:59:38: 2000000 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 12:59:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392424/SRX8392424.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392424/SRX8392424.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392424/SRX8392424.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392424/SRX8392424.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 12:59:45: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:59:45: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:59:49: 6000000 INFO @ Sat, 08 Aug 2020 12:59:49: 3000000 INFO @ Sat, 08 Aug 2020 12:59:57: 1000000 INFO @ Sat, 08 Aug 2020 13:00:01: 7000000 INFO @ Sat, 08 Aug 2020 13:00:01: 4000000 INFO @ Sat, 08 Aug 2020 13:00:09: 2000000 INFO @ Sat, 08 Aug 2020 13:00:12: 8000000 INFO @ Sat, 08 Aug 2020 13:00:13: 5000000 INFO @ Sat, 08 Aug 2020 13:00:19: 3000000 INFO @ Sat, 08 Aug 2020 13:00:24: 6000000 INFO @ Sat, 08 Aug 2020 13:00:24: 9000000 INFO @ Sat, 08 Aug 2020 13:00:30: 4000000 INFO @ Sat, 08 Aug 2020 13:00:36: 10000000 INFO @ Sat, 08 Aug 2020 13:00:37: 7000000 INFO @ Sat, 08 Aug 2020 13:00:41: 5000000 INFO @ Sat, 08 Aug 2020 13:00:48: 11000000 INFO @ Sat, 08 Aug 2020 13:00:49: 8000000 INFO @ Sat, 08 Aug 2020 13:00:52: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:00:56: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:00:56: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:00:56: #1 total tags in treatment: 4600409 INFO @ Sat, 08 Aug 2020 13:00:56: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:00:56: #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 13:00:56: #1 tags after filtering in treatment: 4190647 INFO @ Sat, 08 Aug 2020 13:00:56: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 08 Aug 2020 13:00:56: #1 finished! INFO @ Sat, 08 Aug 2020 13:00:56: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:00:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:00:56: #2 number of paired peaks: 517 WARNING @ Sat, 08 Aug 2020 13:00:56: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Sat, 08 Aug 2020 13:00:56: start model_add_line... INFO @ Sat, 08 Aug 2020 13:00:56: start X-correlation... INFO @ Sat, 08 Aug 2020 13:00:56: end of X-cor INFO @ Sat, 08 Aug 2020 13:00:56: #2 finished! INFO @ Sat, 08 Aug 2020 13:00:56: #2 predicted fragment length is 199 bps INFO @ Sat, 08 Aug 2020 13:00:56: #2 alternative fragment length(s) may be 199 bps INFO @ Sat, 08 Aug 2020 13:00:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392424/SRX8392424.05_model.r WARNING @ Sat, 08 Aug 2020 13:00:56: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:00:56: #2 You may need to consider one of the other alternative d(s): 199 WARNING @ Sat, 08 Aug 2020 13:00:56: #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 13:00:56: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:00:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:01:00: 9000000 INFO @ Sat, 08 Aug 2020 13:01:03: 7000000 INFO @ Sat, 08 Aug 2020 13:01:06: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:01:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392424/SRX8392424.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:01:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392424/SRX8392424.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:01:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392424/SRX8392424.05_summits.bed INFO @ Sat, 08 Aug 2020 13:01:11: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (558 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:01:12: 10000000 INFO @ Sat, 08 Aug 2020 13:01:13: 8000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:01:24: 9000000 INFO @ Sat, 08 Aug 2020 13:01:24: 11000000 INFO @ Sat, 08 Aug 2020 13:01:32: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:01:32: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:01:32: #1 total tags in treatment: 4600409 INFO @ Sat, 08 Aug 2020 13:01:32: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:01:32: #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 13:01:32: #1 tags after filtering in treatment: 4190647 INFO @ Sat, 08 Aug 2020 13:01:32: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 08 Aug 2020 13:01:32: #1 finished! INFO @ Sat, 08 Aug 2020 13:01:32: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:01:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:01:32: #2 number of paired peaks: 517 WARNING @ Sat, 08 Aug 2020 13:01:32: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Sat, 08 Aug 2020 13:01:32: start model_add_line... INFO @ Sat, 08 Aug 2020 13:01:32: start X-correlation... INFO @ Sat, 08 Aug 2020 13:01:32: end of X-cor INFO @ Sat, 08 Aug 2020 13:01:32: #2 finished! INFO @ Sat, 08 Aug 2020 13:01:32: #2 predicted fragment length is 199 bps INFO @ Sat, 08 Aug 2020 13:01:32: #2 alternative fragment length(s) may be 199 bps INFO @ Sat, 08 Aug 2020 13:01:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392424/SRX8392424.10_model.r WARNING @ Sat, 08 Aug 2020 13:01:32: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:01:32: #2 You may need to consider one of the other alternative d(s): 199 WARNING @ Sat, 08 Aug 2020 13:01:32: #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 13:01:32: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:01:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:01:34: 10000000 INFO @ Sat, 08 Aug 2020 13:01:42: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:01:42: 11000000 INFO @ Sat, 08 Aug 2020 13:01:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392424/SRX8392424.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:01:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392424/SRX8392424.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:01:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392424/SRX8392424.10_summits.bed INFO @ Sat, 08 Aug 2020 13:01:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (303 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:01:47: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:01:47: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:01:47: #1 total tags in treatment: 4600409 INFO @ Sat, 08 Aug 2020 13:01:47: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:01:47: #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 13:01:47: #1 tags after filtering in treatment: 4190647 INFO @ Sat, 08 Aug 2020 13:01:47: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 08 Aug 2020 13:01:47: #1 finished! INFO @ Sat, 08 Aug 2020 13:01:47: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:01:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:01:48: #2 number of paired peaks: 517 WARNING @ Sat, 08 Aug 2020 13:01:48: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Sat, 08 Aug 2020 13:01:48: start model_add_line... INFO @ Sat, 08 Aug 2020 13:01:48: start X-correlation... INFO @ Sat, 08 Aug 2020 13:01:48: end of X-cor INFO @ Sat, 08 Aug 2020 13:01:48: #2 finished! INFO @ Sat, 08 Aug 2020 13:01:48: #2 predicted fragment length is 199 bps INFO @ Sat, 08 Aug 2020 13:01:48: #2 alternative fragment length(s) may be 199 bps INFO @ Sat, 08 Aug 2020 13:01:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392424/SRX8392424.20_model.r WARNING @ Sat, 08 Aug 2020 13:01:48: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:01:48: #2 You may need to consider one of the other alternative d(s): 199 WARNING @ Sat, 08 Aug 2020 13:01:48: #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 13:01:48: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:01:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:01:58: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:02:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392424/SRX8392424.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:02:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392424/SRX8392424.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:02:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392424/SRX8392424.20_summits.bed INFO @ Sat, 08 Aug 2020 13:02:02: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (204 records, 4 fields): 2 millis CompletedMACS2peakCalling