Job ID = 6527413 SRX = SRX494841 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:38:26 prefetch.2.10.7: 1) Downloading 'SRR1198373'... 2020-06-29T12:38:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:43:48 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:43:48 prefetch.2.10.7: 1) 'SRR1198373' was downloaded successfully Read 21509609 spots for SRR1198373/SRR1198373.sra Written 21509609 spots for SRR1198373/SRR1198373.sra 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: 00:04:04 21509609 reads; of these: 21509609 (100.00%) were unpaired; of these: 256440 (1.19%) aligned 0 times 17820647 (82.85%) aligned exactly 1 time 3432522 (15.96%) aligned >1 times 98.81% overall alignment rate Time searching: 00:04:04 Overall time: 00:04:04 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 8 files... [bam_rmdupse_core] 3667163 / 21253169 = 0.1725 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 @ Mon, 29 Jun 2020 22:00:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494841/SRX494841.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494841/SRX494841.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494841/SRX494841.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494841/SRX494841.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 @ Mon, 29 Jun 2020 22:00:59: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:00:59: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:01:04: 1000000 INFO @ Mon, 29 Jun 2020 22:01:09: 2000000 INFO @ Mon, 29 Jun 2020 22:01:14: 3000000 INFO @ Mon, 29 Jun 2020 22:01:19: 4000000 INFO @ Mon, 29 Jun 2020 22:01:23: 5000000 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 @ Mon, 29 Jun 2020 22:01:28: 6000000 INFO @ Mon, 29 Jun 2020 22:01:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494841/SRX494841.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494841/SRX494841.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494841/SRX494841.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494841/SRX494841.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 @ Mon, 29 Jun 2020 22:01:29: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:01:29: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:01:33: 7000000 INFO @ Mon, 29 Jun 2020 22:01:35: 1000000 INFO @ Mon, 29 Jun 2020 22:01:38: 8000000 INFO @ Mon, 29 Jun 2020 22:01:39: 2000000 INFO @ Mon, 29 Jun 2020 22:01:43: 9000000 INFO @ Mon, 29 Jun 2020 22:01:44: 3000000 INFO @ Mon, 29 Jun 2020 22:01:47: 10000000 INFO @ Mon, 29 Jun 2020 22:01:49: 4000000 INFO @ Mon, 29 Jun 2020 22:01:52: 11000000 INFO @ Mon, 29 Jun 2020 22:01:54: 5000000 BedGraph に変換中... INFO @ Mon, 29 Jun 2020 22:01:57: 12000000 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 @ Mon, 29 Jun 2020 22:01:59: 6000000 INFO @ Mon, 29 Jun 2020 22:01:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494841/SRX494841.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494841/SRX494841.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494841/SRX494841.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494841/SRX494841.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 @ Mon, 29 Jun 2020 22:01:59: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:01:59: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:02:02: 13000000 INFO @ Mon, 29 Jun 2020 22:02:03: 7000000 INFO @ Mon, 29 Jun 2020 22:02:05: 1000000 INFO @ Mon, 29 Jun 2020 22:02:08: 14000000 INFO @ Mon, 29 Jun 2020 22:02:09: 8000000 INFO @ Mon, 29 Jun 2020 22:02:10: 2000000 INFO @ Mon, 29 Jun 2020 22:02:13: 15000000 INFO @ Mon, 29 Jun 2020 22:02:14: 9000000 INFO @ Mon, 29 Jun 2020 22:02:15: 3000000 INFO @ Mon, 29 Jun 2020 22:02:18: 16000000 INFO @ Mon, 29 Jun 2020 22:02:20: 10000000 INFO @ Mon, 29 Jun 2020 22:02:21: 4000000 INFO @ Mon, 29 Jun 2020 22:02:24: 17000000 INFO @ Mon, 29 Jun 2020 22:02:25: 11000000 INFO @ Mon, 29 Jun 2020 22:02:26: 5000000 INFO @ Mon, 29 Jun 2020 22:02:27: #1 tag size is determined as 42 bps INFO @ Mon, 29 Jun 2020 22:02:27: #1 tag size = 42 INFO @ Mon, 29 Jun 2020 22:02:27: #1 total tags in treatment: 17586006 INFO @ Mon, 29 Jun 2020 22:02:27: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:02:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:02:27: #1 tags after filtering in treatment: 17586006 INFO @ Mon, 29 Jun 2020 22:02:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:02:27: #1 finished! INFO @ Mon, 29 Jun 2020 22:02:27: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:02:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:02:28: #2 number of paired peaks: 224 WARNING @ Mon, 29 Jun 2020 22:02:28: Fewer paired peaks (224) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 224 pairs to build model! INFO @ Mon, 29 Jun 2020 22:02:28: start model_add_line... INFO @ Mon, 29 Jun 2020 22:02:29: start X-correlation... INFO @ Mon, 29 Jun 2020 22:02:29: end of X-cor INFO @ Mon, 29 Jun 2020 22:02:29: #2 finished! INFO @ Mon, 29 Jun 2020 22:02:29: #2 predicted fragment length is 38 bps INFO @ Mon, 29 Jun 2020 22:02:29: #2 alternative fragment length(s) may be 1,38 bps INFO @ Mon, 29 Jun 2020 22:02:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494841/SRX494841.05_model.r WARNING @ Mon, 29 Jun 2020 22:02:29: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:02:29: #2 You may need to consider one of the other alternative d(s): 1,38 WARNING @ Mon, 29 Jun 2020 22:02:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:02:29: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:02:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:02:31: 12000000 INFO @ Mon, 29 Jun 2020 22:02:31: 6000000 INFO @ Mon, 29 Jun 2020 22:02:36: 7000000 INFO @ Mon, 29 Jun 2020 22:02:36: 13000000 INFO @ Mon, 29 Jun 2020 22:02:41: 8000000 INFO @ Mon, 29 Jun 2020 22:02:42: 14000000 INFO @ Mon, 29 Jun 2020 22:02:47: 9000000 INFO @ Mon, 29 Jun 2020 22:02:47: 15000000 INFO @ Mon, 29 Jun 2020 22:02:52: 10000000 INFO @ Mon, 29 Jun 2020 22:02:53: 16000000 INFO @ Mon, 29 Jun 2020 22:02:58: 11000000 INFO @ Mon, 29 Jun 2020 22:02:58: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:02:59: 17000000 INFO @ Mon, 29 Jun 2020 22:03:02: #1 tag size is determined as 42 bps INFO @ Mon, 29 Jun 2020 22:03:02: #1 tag size = 42 INFO @ Mon, 29 Jun 2020 22:03:02: #1 total tags in treatment: 17586006 INFO @ Mon, 29 Jun 2020 22:03:02: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:03:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:03:02: #1 tags after filtering in treatment: 17586006 INFO @ Mon, 29 Jun 2020 22:03:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:03:02: #1 finished! INFO @ Mon, 29 Jun 2020 22:03:02: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:03:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:03:03: 12000000 INFO @ Mon, 29 Jun 2020 22:03:03: #2 number of paired peaks: 224 WARNING @ Mon, 29 Jun 2020 22:03:03: Fewer paired peaks (224) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 224 pairs to build model! INFO @ Mon, 29 Jun 2020 22:03:03: start model_add_line... INFO @ Mon, 29 Jun 2020 22:03:04: start X-correlation... INFO @ Mon, 29 Jun 2020 22:03:04: end of X-cor INFO @ Mon, 29 Jun 2020 22:03:04: #2 finished! INFO @ Mon, 29 Jun 2020 22:03:04: #2 predicted fragment length is 38 bps INFO @ Mon, 29 Jun 2020 22:03:04: #2 alternative fragment length(s) may be 1,38 bps INFO @ Mon, 29 Jun 2020 22:03:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494841/SRX494841.10_model.r WARNING @ Mon, 29 Jun 2020 22:03:04: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:03:04: #2 You may need to consider one of the other alternative d(s): 1,38 WARNING @ Mon, 29 Jun 2020 22:03:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:03:04: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:03:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:03:09: 13000000 INFO @ Mon, 29 Jun 2020 22:03:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494841/SRX494841.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:03:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494841/SRX494841.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:03:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494841/SRX494841.05_summits.bed INFO @ Mon, 29 Jun 2020 22:03:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (705 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:03:14: 14000000 INFO @ Mon, 29 Jun 2020 22:03:20: 15000000 INFO @ Mon, 29 Jun 2020 22:03:25: 16000000 INFO @ Mon, 29 Jun 2020 22:03:31: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:03:33: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:03:34: #1 tag size is determined as 42 bps INFO @ Mon, 29 Jun 2020 22:03:34: #1 tag size = 42 INFO @ Mon, 29 Jun 2020 22:03:34: #1 total tags in treatment: 17586006 INFO @ Mon, 29 Jun 2020 22:03:34: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:03:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:03:34: #1 tags after filtering in treatment: 17586006 INFO @ Mon, 29 Jun 2020 22:03:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:03:34: #1 finished! INFO @ Mon, 29 Jun 2020 22:03:34: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:03:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:03:36: #2 number of paired peaks: 224 WARNING @ Mon, 29 Jun 2020 22:03:36: Fewer paired peaks (224) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 224 pairs to build model! INFO @ Mon, 29 Jun 2020 22:03:36: start model_add_line... INFO @ Mon, 29 Jun 2020 22:03:36: start X-correlation... INFO @ Mon, 29 Jun 2020 22:03:36: end of X-cor INFO @ Mon, 29 Jun 2020 22:03:36: #2 finished! INFO @ Mon, 29 Jun 2020 22:03:36: #2 predicted fragment length is 38 bps INFO @ Mon, 29 Jun 2020 22:03:36: #2 alternative fragment length(s) may be 1,38 bps INFO @ Mon, 29 Jun 2020 22:03:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494841/SRX494841.20_model.r WARNING @ Mon, 29 Jun 2020 22:03:36: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:03:36: #2 You may need to consider one of the other alternative d(s): 1,38 WARNING @ Mon, 29 Jun 2020 22:03:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:03:36: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:03:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:03:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494841/SRX494841.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:03:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494841/SRX494841.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:03:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494841/SRX494841.10_summits.bed INFO @ Mon, 29 Jun 2020 22:03:49: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (334 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:04:05: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:04:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494841/SRX494841.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:04:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494841/SRX494841.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:04:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494841/SRX494841.20_summits.bed INFO @ Mon, 29 Jun 2020 22:04:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (97 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。