Job ID = 6497410 SRX = SRX494822 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T21:52:14 prefetch.2.10.7: 1) Downloading 'SRR1198354'... 2020-06-25T21:52:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:54:11 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:54:12 prefetch.2.10.7: 'SRR1198354' is valid 2020-06-25T21:54:12 prefetch.2.10.7: 1) 'SRR1198354' was downloaded successfully Read 16560194 spots for SRR1198354/SRR1198354.sra Written 16560194 spots for SRR1198354/SRR1198354.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: 00:02:55 16560194 reads; of these: 16560194 (100.00%) were unpaired; of these: 532550 (3.22%) aligned 0 times 13113713 (79.19%) aligned exactly 1 time 2913931 (17.60%) aligned >1 times 96.78% overall alignment rate Time searching: 00:02:57 Overall time: 00:02:57 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_rmdupse_core] 1975799 / 16027644 = 0.1233 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 @ Fri, 26 Jun 2020 07:01:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494822/SRX494822.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494822/SRX494822.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494822/SRX494822.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494822/SRX494822.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 @ Fri, 26 Jun 2020 07:01:34: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:01:34: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:01:39: 1000000 INFO @ Fri, 26 Jun 2020 07:01:44: 2000000 INFO @ Fri, 26 Jun 2020 07:01:50: 3000000 INFO @ Fri, 26 Jun 2020 07:01:55: 4000000 INFO @ Fri, 26 Jun 2020 07:02:00: 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 @ Fri, 26 Jun 2020 07:02:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494822/SRX494822.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494822/SRX494822.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494822/SRX494822.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494822/SRX494822.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 @ Fri, 26 Jun 2020 07:02:04: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:02:04: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:02:06: 6000000 INFO @ Fri, 26 Jun 2020 07:02:11: 1000000 INFO @ Fri, 26 Jun 2020 07:02:12: 7000000 INFO @ Fri, 26 Jun 2020 07:02:18: 2000000 INFO @ Fri, 26 Jun 2020 07:02:18: 8000000 INFO @ Fri, 26 Jun 2020 07:02:24: 9000000 INFO @ Fri, 26 Jun 2020 07:02:25: 3000000 INFO @ Fri, 26 Jun 2020 07:02:31: 10000000 INFO @ Fri, 26 Jun 2020 07:02:32: 4000000 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 @ Fri, 26 Jun 2020 07:02:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494822/SRX494822.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494822/SRX494822.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494822/SRX494822.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494822/SRX494822.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 @ Fri, 26 Jun 2020 07:02:34: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:02:34: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:02:37: 11000000 INFO @ Fri, 26 Jun 2020 07:02:39: 5000000 INFO @ Fri, 26 Jun 2020 07:02:41: 1000000 INFO @ Fri, 26 Jun 2020 07:02:43: 12000000 INFO @ Fri, 26 Jun 2020 07:02:46: 6000000 INFO @ Fri, 26 Jun 2020 07:02:48: 2000000 INFO @ Fri, 26 Jun 2020 07:02:50: 13000000 INFO @ Fri, 26 Jun 2020 07:02:53: 7000000 INFO @ Fri, 26 Jun 2020 07:02:55: 3000000 INFO @ Fri, 26 Jun 2020 07:02:56: 14000000 INFO @ Fri, 26 Jun 2020 07:02:56: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:02:56: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:02:56: #1 total tags in treatment: 14051845 INFO @ Fri, 26 Jun 2020 07:02:56: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:02:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:02:57: #1 tags after filtering in treatment: 14051845 INFO @ Fri, 26 Jun 2020 07:02:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:02:57: #1 finished! INFO @ Fri, 26 Jun 2020 07:02:57: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:02:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:02:58: #2 number of paired peaks: 257 WARNING @ Fri, 26 Jun 2020 07:02:58: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Fri, 26 Jun 2020 07:02:58: start model_add_line... INFO @ Fri, 26 Jun 2020 07:02:58: start X-correlation... INFO @ Fri, 26 Jun 2020 07:02:58: end of X-cor INFO @ Fri, 26 Jun 2020 07:02:58: #2 finished! INFO @ Fri, 26 Jun 2020 07:02:58: #2 predicted fragment length is 35 bps INFO @ Fri, 26 Jun 2020 07:02:58: #2 alternative fragment length(s) may be 1,35 bps INFO @ Fri, 26 Jun 2020 07:02:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494822/SRX494822.05_model.r INFO @ Fri, 26 Jun 2020 07:02:59: 8000000 INFO @ Fri, 26 Jun 2020 07:03:02: 4000000 INFO @ Fri, 26 Jun 2020 07:03:06: 9000000 INFO @ Fri, 26 Jun 2020 07:03:08: 5000000 WARNING @ Fri, 26 Jun 2020 07:03:11: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:03:11: #2 You may need to consider one of the other alternative d(s): 1,35 WARNING @ Fri, 26 Jun 2020 07:03:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:03:11: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:03:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:03:13: 10000000 INFO @ Fri, 26 Jun 2020 07:03:15: 6000000 INFO @ Fri, 26 Jun 2020 07:03:19: 11000000 INFO @ Fri, 26 Jun 2020 07:03:22: 7000000 INFO @ Fri, 26 Jun 2020 07:03:26: 12000000 INFO @ Fri, 26 Jun 2020 07:03:29: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:03:33: 13000000 INFO @ Fri, 26 Jun 2020 07:03:35: 9000000 INFO @ Fri, 26 Jun 2020 07:03:37: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:03:39: 14000000 INFO @ Fri, 26 Jun 2020 07:03:40: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:03:40: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:03:40: #1 total tags in treatment: 14051845 INFO @ Fri, 26 Jun 2020 07:03:40: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:03:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:03:40: #1 tags after filtering in treatment: 14051845 INFO @ Fri, 26 Jun 2020 07:03:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:03:40: #1 finished! INFO @ Fri, 26 Jun 2020 07:03:40: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:03:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:03:41: #2 number of paired peaks: 257 WARNING @ Fri, 26 Jun 2020 07:03:41: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Fri, 26 Jun 2020 07:03:41: start model_add_line... INFO @ Fri, 26 Jun 2020 07:03:41: start X-correlation... INFO @ Fri, 26 Jun 2020 07:03:41: end of X-cor INFO @ Fri, 26 Jun 2020 07:03:41: #2 finished! INFO @ Fri, 26 Jun 2020 07:03:41: #2 predicted fragment length is 35 bps INFO @ Fri, 26 Jun 2020 07:03:41: #2 alternative fragment length(s) may be 1,35 bps INFO @ Fri, 26 Jun 2020 07:03:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494822/SRX494822.10_model.r WARNING @ Fri, 26 Jun 2020 07:03:41: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:03:41: #2 You may need to consider one of the other alternative d(s): 1,35 WARNING @ Fri, 26 Jun 2020 07:03:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:03:41: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:03:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:03:42: 10000000 INFO @ Fri, 26 Jun 2020 07:03:48: 11000000 INFO @ Fri, 26 Jun 2020 07:03:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494822/SRX494822.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:03:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494822/SRX494822.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:03:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494822/SRX494822.05_summits.bed INFO @ Fri, 26 Jun 2020 07:03:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1347 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:03:55: 12000000 INFO @ Fri, 26 Jun 2020 07:04:01: 13000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:04:06: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:04:07: 14000000 INFO @ Fri, 26 Jun 2020 07:04:07: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:04:07: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:04:07: #1 total tags in treatment: 14051845 INFO @ Fri, 26 Jun 2020 07:04:07: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:04:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:04:08: #1 tags after filtering in treatment: 14051845 INFO @ Fri, 26 Jun 2020 07:04:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:04:08: #1 finished! INFO @ Fri, 26 Jun 2020 07:04:08: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:04:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:04:09: #2 number of paired peaks: 257 WARNING @ Fri, 26 Jun 2020 07:04:09: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Fri, 26 Jun 2020 07:04:09: start model_add_line... INFO @ Fri, 26 Jun 2020 07:04:09: start X-correlation... INFO @ Fri, 26 Jun 2020 07:04:09: end of X-cor INFO @ Fri, 26 Jun 2020 07:04:09: #2 finished! INFO @ Fri, 26 Jun 2020 07:04:09: #2 predicted fragment length is 35 bps INFO @ Fri, 26 Jun 2020 07:04:09: #2 alternative fragment length(s) may be 1,35 bps INFO @ Fri, 26 Jun 2020 07:04:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494822/SRX494822.20_model.r WARNING @ Fri, 26 Jun 2020 07:04:09: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:04:09: #2 You may need to consider one of the other alternative d(s): 1,35 WARNING @ Fri, 26 Jun 2020 07:04:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:04:09: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:04:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:04:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494822/SRX494822.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:04:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494822/SRX494822.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:04:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494822/SRX494822.10_summits.bed INFO @ Fri, 26 Jun 2020 07:04:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (578 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:04:33: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:04:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494822/SRX494822.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:04:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494822/SRX494822.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:04:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494822/SRX494822.20_summits.bed INFO @ Fri, 26 Jun 2020 07:04:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (124 records, 4 fields): 1 millis CompletedMACS2peakCalling