Job ID = 8069447 SRX = SRX8392425 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:33:10 prefetch.2.10.7: 1) Downloading 'SRR11842078'... 2020-08-08T03:33:10 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:35:34 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:35:34 prefetch.2.10.7: 1) 'SRR11842078' was downloaded successfully 2020-08-08T03:35:34 prefetch.2.10.7: 'SRR11842078' has 0 unresolved dependencies Read 8317636 spots for SRR11842078/SRR11842078.sra Written 8317636 spots for SRR11842078/SRR11842078.sra fastq に変換しました。 bowtie でマッピング中... Your job 8070424 ("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: 00:14:03 8317636 reads; of these: 8317636 (100.00%) were paired; of these: 2838918 (34.13%) aligned concordantly 0 times 4676360 (56.22%) aligned concordantly exactly 1 time 802358 (9.65%) aligned concordantly >1 times ---- 2838918 pairs aligned concordantly 0 times; of these: 972495 (34.26%) aligned discordantly 1 time ---- 1866423 pairs aligned 0 times concordantly or discordantly; of these: 3732846 mates make up the pairs; of these: 3416223 (91.52%) aligned 0 times 139276 (3.73%) aligned exactly 1 time 177347 (4.75%) aligned >1 times 79.46% overall alignment rate Time searching: 00:14:03 Overall time: 00:14:03 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] 1284514 / 6396214 = 0.2008 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 12:56:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392425/SRX8392425.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392425/SRX8392425.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392425/SRX8392425.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392425/SRX8392425.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 12:56:15: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:56:15: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:56:23: 1000000 INFO @ Sat, 08 Aug 2020 12:56:32: 2000000 INFO @ Sat, 08 Aug 2020 12:56:41: 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 12:56:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392425/SRX8392425.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392425/SRX8392425.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392425/SRX8392425.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392425/SRX8392425.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 12:56:45: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:56:45: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:56:50: 4000000 INFO @ Sat, 08 Aug 2020 12:56:53: 1000000 INFO @ Sat, 08 Aug 2020 12:57:00: 5000000 INFO @ Sat, 08 Aug 2020 12:57:01: 2000000 INFO @ Sat, 08 Aug 2020 12:57:09: 3000000 INFO @ Sat, 08 Aug 2020 12:57:09: 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 12:57:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392425/SRX8392425.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392425/SRX8392425.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392425/SRX8392425.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392425/SRX8392425.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 12:57:15: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:57:15: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:57:17: 4000000 INFO @ Sat, 08 Aug 2020 12:57:19: 7000000 INFO @ Sat, 08 Aug 2020 12:57:24: 1000000 INFO @ Sat, 08 Aug 2020 12:57:25: 5000000 INFO @ Sat, 08 Aug 2020 12:57:28: 8000000 INFO @ Sat, 08 Aug 2020 12:57:33: 6000000 INFO @ Sat, 08 Aug 2020 12:57:33: 2000000 INFO @ Sat, 08 Aug 2020 12:57:37: 9000000 INFO @ Sat, 08 Aug 2020 12:57:41: 7000000 INFO @ Sat, 08 Aug 2020 12:57:42: 3000000 INFO @ Sat, 08 Aug 2020 12:57:47: 10000000 INFO @ Sat, 08 Aug 2020 12:57:49: 8000000 INFO @ Sat, 08 Aug 2020 12:57:52: 4000000 INFO @ Sat, 08 Aug 2020 12:57:53: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:57:53: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:57:53: #1 total tags in treatment: 4349914 INFO @ Sat, 08 Aug 2020 12:57:53: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:57:53: #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 12:57:53: #1 tags after filtering in treatment: 4037039 INFO @ Sat, 08 Aug 2020 12:57:53: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Aug 2020 12:57:53: #1 finished! INFO @ Sat, 08 Aug 2020 12:57:53: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:57:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:57:53: #2 number of paired peaks: 476 WARNING @ Sat, 08 Aug 2020 12:57:53: Fewer paired peaks (476) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 476 pairs to build model! INFO @ Sat, 08 Aug 2020 12:57:53: start model_add_line... INFO @ Sat, 08 Aug 2020 12:57:53: start X-correlation... INFO @ Sat, 08 Aug 2020 12:57:53: end of X-cor INFO @ Sat, 08 Aug 2020 12:57:53: #2 finished! INFO @ Sat, 08 Aug 2020 12:57:53: #2 predicted fragment length is 201 bps INFO @ Sat, 08 Aug 2020 12:57:53: #2 alternative fragment length(s) may be 201 bps INFO @ Sat, 08 Aug 2020 12:57:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392425/SRX8392425.05_model.r WARNING @ Sat, 08 Aug 2020 12:57:53: #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 12:57:53: #2 You may need to consider one of the other alternative d(s): 201 WARNING @ Sat, 08 Aug 2020 12:57:53: #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 12:57:53: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:57:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:57:58: 9000000 INFO @ Sat, 08 Aug 2020 12:58:02: 5000000 INFO @ Sat, 08 Aug 2020 12:58:02: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:58:06: 10000000 INFO @ Sat, 08 Aug 2020 12:58:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392425/SRX8392425.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:58:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392425/SRX8392425.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:58:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392425/SRX8392425.05_summits.bed INFO @ Sat, 08 Aug 2020 12:58:06: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (355 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:58:11: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:58:11: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:58:11: #1 total tags in treatment: 4349914 INFO @ Sat, 08 Aug 2020 12:58:11: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:58:11: #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 12:58:11: #1 tags after filtering in treatment: 4037039 INFO @ Sat, 08 Aug 2020 12:58:11: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Aug 2020 12:58:11: #1 finished! INFO @ Sat, 08 Aug 2020 12:58:11: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:58:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:58:11: #2 number of paired peaks: 476 WARNING @ Sat, 08 Aug 2020 12:58:11: Fewer paired peaks (476) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 476 pairs to build model! INFO @ Sat, 08 Aug 2020 12:58:11: start model_add_line... INFO @ Sat, 08 Aug 2020 12:58:11: start X-correlation... INFO @ Sat, 08 Aug 2020 12:58:11: end of X-cor INFO @ Sat, 08 Aug 2020 12:58:11: #2 finished! INFO @ Sat, 08 Aug 2020 12:58:11: #2 predicted fragment length is 201 bps INFO @ Sat, 08 Aug 2020 12:58:11: #2 alternative fragment length(s) may be 201 bps INFO @ Sat, 08 Aug 2020 12:58:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392425/SRX8392425.10_model.r WARNING @ Sat, 08 Aug 2020 12:58:11: #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 12:58:11: #2 You may need to consider one of the other alternative d(s): 201 WARNING @ Sat, 08 Aug 2020 12:58:11: #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 12:58:11: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:58:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:58:12: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 12:58:21: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:58:22: 7000000 INFO @ Sat, 08 Aug 2020 12:58:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392425/SRX8392425.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:58:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392425/SRX8392425.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:58:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392425/SRX8392425.10_summits.bed INFO @ Sat, 08 Aug 2020 12:58:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (258 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:58:30: 8000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:58:39: 9000000 INFO @ Sat, 08 Aug 2020 12:58:48: 10000000 INFO @ Sat, 08 Aug 2020 12:58:53: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:58:53: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:58:53: #1 total tags in treatment: 4349914 INFO @ Sat, 08 Aug 2020 12:58:53: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:58:53: #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 12:58:53: #1 tags after filtering in treatment: 4037039 INFO @ Sat, 08 Aug 2020 12:58:53: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Aug 2020 12:58:53: #1 finished! INFO @ Sat, 08 Aug 2020 12:58:53: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:58:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:58:53: #2 number of paired peaks: 476 WARNING @ Sat, 08 Aug 2020 12:58:53: Fewer paired peaks (476) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 476 pairs to build model! INFO @ Sat, 08 Aug 2020 12:58:53: start model_add_line... INFO @ Sat, 08 Aug 2020 12:58:53: start X-correlation... INFO @ Sat, 08 Aug 2020 12:58:53: end of X-cor INFO @ Sat, 08 Aug 2020 12:58:53: #2 finished! INFO @ Sat, 08 Aug 2020 12:58:53: #2 predicted fragment length is 201 bps INFO @ Sat, 08 Aug 2020 12:58:53: #2 alternative fragment length(s) may be 201 bps INFO @ Sat, 08 Aug 2020 12:58:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392425/SRX8392425.20_model.r WARNING @ Sat, 08 Aug 2020 12:58:53: #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 12:58:53: #2 You may need to consider one of the other alternative d(s): 201 WARNING @ Sat, 08 Aug 2020 12:58:53: #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 12:58:53: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:58:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:59:03: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:59:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392425/SRX8392425.20_peaks.xls INFO @ Sat, 08 Aug 2020 12:59:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392425/SRX8392425.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:59:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392425/SRX8392425.20_summits.bed INFO @ Sat, 08 Aug 2020 12:59:07: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (186 records, 4 fields): 1 millis CompletedMACS2peakCalling