Job ID = 8069419 SRX = SRX8392416 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:32:45 prefetch.2.10.7: 1) Downloading 'SRR11842069'... 2020-08-08T03:32:45 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:34:57 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:34:57 prefetch.2.10.7: 1) 'SRR11842069' was downloaded successfully 2020-08-08T03:34:57 prefetch.2.10.7: 'SRR11842069' has 0 unresolved dependencies Read 8897514 spots for SRR11842069/SRR11842069.sra Written 8897514 spots for SRR11842069/SRR11842069.sra fastq に変換しました。 bowtie でマッピング中... Your job 8070393 ("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: 00:14:09 8897514 reads; of these: 8897514 (100.00%) were paired; of these: 2528620 (28.42%) aligned concordantly 0 times 5507943 (61.90%) aligned concordantly exactly 1 time 860951 (9.68%) aligned concordantly >1 times ---- 2528620 pairs aligned concordantly 0 times; of these: 413366 (16.35%) aligned discordantly 1 time ---- 2115254 pairs aligned 0 times concordantly or discordantly; of these: 4230508 mates make up the pairs; of these: 4049190 (95.71%) aligned 0 times 93481 (2.21%) aligned exactly 1 time 87837 (2.08%) aligned >1 times 77.25% overall alignment rate Time searching: 00:14:09 Overall time: 00:14:09 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] 1112047 / 6750343 = 0.1647 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 12:55:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392416/SRX8392416.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392416/SRX8392416.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392416/SRX8392416.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392416/SRX8392416.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 12:55:35: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:55:35: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:55:42: 1000000 INFO @ Sat, 08 Aug 2020 12:55:48: 2000000 INFO @ Sat, 08 Aug 2020 12:55:54: 3000000 INFO @ Sat, 08 Aug 2020 12:56:00: 4000000 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 12:56:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392416/SRX8392416.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392416/SRX8392416.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392416/SRX8392416.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392416/SRX8392416.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 12:56:05: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:56:05: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:56:06: 5000000 INFO @ Sat, 08 Aug 2020 12:56:11: 1000000 INFO @ Sat, 08 Aug 2020 12:56:12: 6000000 INFO @ Sat, 08 Aug 2020 12:56:18: 2000000 INFO @ Sat, 08 Aug 2020 12:56:19: 7000000 INFO @ Sat, 08 Aug 2020 12:56:24: 3000000 INFO @ Sat, 08 Aug 2020 12:56:25: 8000000 INFO @ Sat, 08 Aug 2020 12:56:30: 4000000 INFO @ Sat, 08 Aug 2020 12:56:31: 9000000 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 12:56:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392416/SRX8392416.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392416/SRX8392416.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392416/SRX8392416.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392416/SRX8392416.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 12:56:35: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:56:35: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:56:37: 5000000 INFO @ Sat, 08 Aug 2020 12:56:38: 10000000 INFO @ Sat, 08 Aug 2020 12:56:42: 1000000 INFO @ Sat, 08 Aug 2020 12:56:43: 6000000 INFO @ Sat, 08 Aug 2020 12:56:44: 11000000 INFO @ Sat, 08 Aug 2020 12:56:47: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:56:47: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:56:47: #1 total tags in treatment: 5311008 INFO @ Sat, 08 Aug 2020 12:56:47: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:56:47: #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 12:56:47: #1 tags after filtering in treatment: 4968118 INFO @ Sat, 08 Aug 2020 12:56:47: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 08 Aug 2020 12:56:47: #1 finished! INFO @ Sat, 08 Aug 2020 12:56:47: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:56:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:56:48: #2 number of paired peaks: 435 WARNING @ Sat, 08 Aug 2020 12:56:48: Fewer paired peaks (435) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 435 pairs to build model! INFO @ Sat, 08 Aug 2020 12:56:48: start model_add_line... INFO @ Sat, 08 Aug 2020 12:56:48: start X-correlation... INFO @ Sat, 08 Aug 2020 12:56:48: end of X-cor INFO @ Sat, 08 Aug 2020 12:56:48: #2 finished! INFO @ Sat, 08 Aug 2020 12:56:48: #2 predicted fragment length is 211 bps INFO @ Sat, 08 Aug 2020 12:56:48: #2 alternative fragment length(s) may be 211 bps INFO @ Sat, 08 Aug 2020 12:56:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392416/SRX8392416.05_model.r WARNING @ Sat, 08 Aug 2020 12:56:48: #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 12:56:48: #2 You may need to consider one of the other alternative d(s): 211 WARNING @ Sat, 08 Aug 2020 12:56:48: #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 12:56:48: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:56:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:56:49: 7000000 INFO @ Sat, 08 Aug 2020 12:56:50: 2000000 INFO @ Sat, 08 Aug 2020 12:56:56: 8000000 INFO @ Sat, 08 Aug 2020 12:56:58: 3000000 INFO @ Sat, 08 Aug 2020 12:56:59: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:57:02: 9000000 INFO @ Sat, 08 Aug 2020 12:57:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392416/SRX8392416.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:57:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392416/SRX8392416.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:57:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392416/SRX8392416.05_summits.bed INFO @ Sat, 08 Aug 2020 12:57:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (328 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:57:06: 4000000 INFO @ Sat, 08 Aug 2020 12:57:09: 10000000 INFO @ Sat, 08 Aug 2020 12:57:13: 5000000 INFO @ Sat, 08 Aug 2020 12:57:16: 11000000 INFO @ Sat, 08 Aug 2020 12:57:19: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:57:19: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:57:19: #1 total tags in treatment: 5311008 INFO @ Sat, 08 Aug 2020 12:57:19: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:57:19: #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 12:57:19: #1 tags after filtering in treatment: 4968118 INFO @ Sat, 08 Aug 2020 12:57:19: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 08 Aug 2020 12:57:19: #1 finished! INFO @ Sat, 08 Aug 2020 12:57:19: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:57:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:57:19: #2 number of paired peaks: 435 WARNING @ Sat, 08 Aug 2020 12:57:19: Fewer paired peaks (435) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 435 pairs to build model! INFO @ Sat, 08 Aug 2020 12:57:19: start model_add_line... INFO @ Sat, 08 Aug 2020 12:57:19: start X-correlation... INFO @ Sat, 08 Aug 2020 12:57:19: end of X-cor INFO @ Sat, 08 Aug 2020 12:57:19: #2 finished! INFO @ Sat, 08 Aug 2020 12:57:19: #2 predicted fragment length is 211 bps INFO @ Sat, 08 Aug 2020 12:57:19: #2 alternative fragment length(s) may be 211 bps INFO @ Sat, 08 Aug 2020 12:57:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392416/SRX8392416.10_model.r WARNING @ Sat, 08 Aug 2020 12:57:19: #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 12:57:19: #2 You may need to consider one of the other alternative d(s): 211 WARNING @ Sat, 08 Aug 2020 12:57:19: #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 12:57:19: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:57:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:57:21: 6000000 INFO @ Sat, 08 Aug 2020 12:57:29: 7000000 INFO @ Sat, 08 Aug 2020 12:57:30: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:57:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392416/SRX8392416.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:57:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392416/SRX8392416.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:57:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392416/SRX8392416.10_summits.bed INFO @ Sat, 08 Aug 2020 12:57:36: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (248 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:57:37: 8000000 INFO @ Sat, 08 Aug 2020 12:57:44: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 12:57:52: 10000000 INFO @ Sat, 08 Aug 2020 12:58:00: 11000000 INFO @ Sat, 08 Aug 2020 12:58:04: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:58:04: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:58:04: #1 total tags in treatment: 5311008 INFO @ Sat, 08 Aug 2020 12:58:04: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:58:04: #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 12:58:04: #1 tags after filtering in treatment: 4968118 INFO @ Sat, 08 Aug 2020 12:58:04: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 08 Aug 2020 12:58:04: #1 finished! INFO @ Sat, 08 Aug 2020 12:58:04: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:58:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:58:04: #2 number of paired peaks: 435 WARNING @ Sat, 08 Aug 2020 12:58:04: Fewer paired peaks (435) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 435 pairs to build model! INFO @ Sat, 08 Aug 2020 12:58:04: start model_add_line... INFO @ Sat, 08 Aug 2020 12:58:04: start X-correlation... INFO @ Sat, 08 Aug 2020 12:58:04: end of X-cor INFO @ Sat, 08 Aug 2020 12:58:04: #2 finished! INFO @ Sat, 08 Aug 2020 12:58:04: #2 predicted fragment length is 211 bps INFO @ Sat, 08 Aug 2020 12:58:04: #2 alternative fragment length(s) may be 211 bps INFO @ Sat, 08 Aug 2020 12:58:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392416/SRX8392416.20_model.r WARNING @ Sat, 08 Aug 2020 12:58:04: #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 12:58:04: #2 You may need to consider one of the other alternative d(s): 211 WARNING @ Sat, 08 Aug 2020 12:58:04: #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 12:58:04: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:58:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:58:15: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:58:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392416/SRX8392416.20_peaks.xls INFO @ Sat, 08 Aug 2020 12:58:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392416/SRX8392416.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:58:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392416/SRX8392416.20_summits.bed INFO @ Sat, 08 Aug 2020 12:58:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (182 records, 4 fields): 3 millis CompletedMACS2peakCalling