Job ID = 6497455 SRX = SRX494952 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T01:43:39 prefetch.2.10.7: 1) Downloading 'SRR1198484'... 2020-06-26T01:43:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T01:45:39 prefetch.2.10.7: HTTPS download succeed 2020-06-26T01:45:39 prefetch.2.10.7: 1) 'SRR1198484' was downloaded successfully Read 33047917 spots for SRR1198484/SRR1198484.sra Written 33047917 spots for SRR1198484/SRR1198484.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:56 33047917 reads; of these: 33047917 (100.00%) were unpaired; of these: 4347993 (13.16%) aligned 0 times 23791605 (71.99%) aligned exactly 1 time 4908319 (14.85%) aligned >1 times 86.84% overall alignment rate Time searching: 00:04:57 Overall time: 00:04:57 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_sort_core] merging from 8 files... [bam_rmdupse_core] 5314291 / 28699924 = 0.1852 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 10:57:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494952/SRX494952.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494952/SRX494952.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494952/SRX494952.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494952/SRX494952.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 10:57:57: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:57:57: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:58:02: 1000000 INFO @ Fri, 26 Jun 2020 10:58:07: 2000000 INFO @ Fri, 26 Jun 2020 10:58:12: 3000000 INFO @ Fri, 26 Jun 2020 10:58:18: 4000000 INFO @ Fri, 26 Jun 2020 10:58:23: 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 @ Fri, 26 Jun 2020 10:58:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494952/SRX494952.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494952/SRX494952.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494952/SRX494952.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494952/SRX494952.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 10:58:26: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:58:26: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:58:28: 6000000 INFO @ Fri, 26 Jun 2020 10:58:31: 1000000 INFO @ Fri, 26 Jun 2020 10:58:33: 7000000 INFO @ Fri, 26 Jun 2020 10:58:37: 2000000 INFO @ Fri, 26 Jun 2020 10:58:39: 8000000 INFO @ Fri, 26 Jun 2020 10:58:42: 3000000 INFO @ Fri, 26 Jun 2020 10:58:44: 9000000 INFO @ Fri, 26 Jun 2020 10:58:48: 4000000 INFO @ Fri, 26 Jun 2020 10:58:50: 10000000 INFO @ Fri, 26 Jun 2020 10:58:54: 5000000 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 10:58:55: 11000000 INFO @ Fri, 26 Jun 2020 10:58:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494952/SRX494952.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494952/SRX494952.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494952/SRX494952.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494952/SRX494952.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 10:58:56: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:58:56: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:58:59: 6000000 INFO @ Fri, 26 Jun 2020 10:59:01: 12000000 INFO @ Fri, 26 Jun 2020 10:59:02: 1000000 INFO @ Fri, 26 Jun 2020 10:59:05: 7000000 INFO @ Fri, 26 Jun 2020 10:59:07: 13000000 INFO @ Fri, 26 Jun 2020 10:59:07: 2000000 INFO @ Fri, 26 Jun 2020 10:59:10: 8000000 INFO @ Fri, 26 Jun 2020 10:59:12: 14000000 INFO @ Fri, 26 Jun 2020 10:59:13: 3000000 INFO @ Fri, 26 Jun 2020 10:59:16: 9000000 INFO @ Fri, 26 Jun 2020 10:59:18: 15000000 INFO @ Fri, 26 Jun 2020 10:59:19: 4000000 INFO @ Fri, 26 Jun 2020 10:59:21: 10000000 INFO @ Fri, 26 Jun 2020 10:59:24: 16000000 INFO @ Fri, 26 Jun 2020 10:59:24: 5000000 INFO @ Fri, 26 Jun 2020 10:59:27: 11000000 INFO @ Fri, 26 Jun 2020 10:59:30: 17000000 INFO @ Fri, 26 Jun 2020 10:59:30: 6000000 INFO @ Fri, 26 Jun 2020 10:59:32: 12000000 INFO @ Fri, 26 Jun 2020 10:59:35: 18000000 INFO @ Fri, 26 Jun 2020 10:59:35: 7000000 INFO @ Fri, 26 Jun 2020 10:59:38: 13000000 INFO @ Fri, 26 Jun 2020 10:59:41: 8000000 INFO @ Fri, 26 Jun 2020 10:59:41: 19000000 INFO @ Fri, 26 Jun 2020 10:59:44: 14000000 INFO @ Fri, 26 Jun 2020 10:59:46: 9000000 INFO @ Fri, 26 Jun 2020 10:59:47: 20000000 INFO @ Fri, 26 Jun 2020 10:59:49: 15000000 INFO @ Fri, 26 Jun 2020 10:59:52: 10000000 INFO @ Fri, 26 Jun 2020 10:59:53: 21000000 INFO @ Fri, 26 Jun 2020 10:59:55: 16000000 INFO @ Fri, 26 Jun 2020 10:59:57: 11000000 INFO @ Fri, 26 Jun 2020 10:59:58: 22000000 INFO @ Fri, 26 Jun 2020 11:00:01: 17000000 INFO @ Fri, 26 Jun 2020 11:00:03: 12000000 INFO @ Fri, 26 Jun 2020 11:00:04: 23000000 INFO @ Fri, 26 Jun 2020 11:00:06: 18000000 INFO @ Fri, 26 Jun 2020 11:00:06: #1 tag size is determined as 35 bps INFO @ Fri, 26 Jun 2020 11:00:06: #1 tag size = 35 INFO @ Fri, 26 Jun 2020 11:00:06: #1 total tags in treatment: 23385633 INFO @ Fri, 26 Jun 2020 11:00:06: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 11:00:06: #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 11:00:07: #1 tags after filtering in treatment: 23385633 INFO @ Fri, 26 Jun 2020 11:00:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 11:00:07: #1 finished! INFO @ Fri, 26 Jun 2020 11:00:07: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 11:00:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 11:00:08: #2 number of paired peaks: 162 WARNING @ Fri, 26 Jun 2020 11:00:08: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Fri, 26 Jun 2020 11:00:08: start model_add_line... INFO @ Fri, 26 Jun 2020 11:00:09: start X-correlation... INFO @ Fri, 26 Jun 2020 11:00:09: end of X-cor INFO @ Fri, 26 Jun 2020 11:00:09: #2 finished! INFO @ Fri, 26 Jun 2020 11:00:09: #2 predicted fragment length is 35 bps INFO @ Fri, 26 Jun 2020 11:00:09: #2 alternative fragment length(s) may be 2,35,586 bps INFO @ Fri, 26 Jun 2020 11:00:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494952/SRX494952.05_model.r WARNING @ Fri, 26 Jun 2020 11:00:09: #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 11:00:09: #2 You may need to consider one of the other alternative d(s): 2,35,586 WARNING @ Fri, 26 Jun 2020 11:00:09: #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 11:00:09: #3 Call peaks... INFO @ Fri, 26 Jun 2020 11:00:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 11:00:09: 13000000 INFO @ Fri, 26 Jun 2020 11:00:12: 19000000 INFO @ Fri, 26 Jun 2020 11:00:14: 14000000 INFO @ Fri, 26 Jun 2020 11:00:18: 20000000 INFO @ Fri, 26 Jun 2020 11:00:20: 15000000 INFO @ Fri, 26 Jun 2020 11:00:23: 21000000 INFO @ Fri, 26 Jun 2020 11:00:26: 16000000 INFO @ Fri, 26 Jun 2020 11:00:29: 22000000 INFO @ Fri, 26 Jun 2020 11:00:31: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 11:00:34: 23000000 INFO @ Fri, 26 Jun 2020 11:00:37: #1 tag size is determined as 35 bps INFO @ Fri, 26 Jun 2020 11:00:37: #1 tag size = 35 INFO @ Fri, 26 Jun 2020 11:00:37: #1 total tags in treatment: 23385633 INFO @ Fri, 26 Jun 2020 11:00:37: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 11:00:37: #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 11:00:37: 18000000 INFO @ Fri, 26 Jun 2020 11:00:37: #1 tags after filtering in treatment: 23385633 INFO @ Fri, 26 Jun 2020 11:00:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 11:00:37: #1 finished! INFO @ Fri, 26 Jun 2020 11:00:37: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 11:00:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 11:00:39: #2 number of paired peaks: 162 WARNING @ Fri, 26 Jun 2020 11:00:39: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Fri, 26 Jun 2020 11:00:39: start model_add_line... INFO @ Fri, 26 Jun 2020 11:00:39: start X-correlation... INFO @ Fri, 26 Jun 2020 11:00:39: end of X-cor INFO @ Fri, 26 Jun 2020 11:00:39: #2 finished! INFO @ Fri, 26 Jun 2020 11:00:39: #2 predicted fragment length is 35 bps INFO @ Fri, 26 Jun 2020 11:00:39: #2 alternative fragment length(s) may be 2,35,586 bps INFO @ Fri, 26 Jun 2020 11:00:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494952/SRX494952.10_model.r WARNING @ Fri, 26 Jun 2020 11:00:39: #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 11:00:39: #2 You may need to consider one of the other alternative d(s): 2,35,586 WARNING @ Fri, 26 Jun 2020 11:00:39: #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 11:00:39: #3 Call peaks... INFO @ Fri, 26 Jun 2020 11:00:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 11:00:42: 19000000 INFO @ Fri, 26 Jun 2020 11:00:47: 20000000 INFO @ Fri, 26 Jun 2020 11:00:51: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 11:00:53: 21000000 INFO @ Fri, 26 Jun 2020 11:00:58: 22000000 INFO @ Fri, 26 Jun 2020 11:01:03: 23000000 INFO @ Fri, 26 Jun 2020 11:01:05: #1 tag size is determined as 35 bps INFO @ Fri, 26 Jun 2020 11:01:05: #1 tag size = 35 INFO @ Fri, 26 Jun 2020 11:01:05: #1 total tags in treatment: 23385633 INFO @ Fri, 26 Jun 2020 11:01:05: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 11:01:05: #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 11:01:06: #1 tags after filtering in treatment: 23385633 INFO @ Fri, 26 Jun 2020 11:01:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 11:01:06: #1 finished! INFO @ Fri, 26 Jun 2020 11:01:06: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 11:01:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 11:01:07: #2 number of paired peaks: 162 WARNING @ Fri, 26 Jun 2020 11:01:07: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Fri, 26 Jun 2020 11:01:07: start model_add_line... INFO @ Fri, 26 Jun 2020 11:01:08: start X-correlation... INFO @ Fri, 26 Jun 2020 11:01:08: end of X-cor INFO @ Fri, 26 Jun 2020 11:01:08: #2 finished! INFO @ Fri, 26 Jun 2020 11:01:08: #2 predicted fragment length is 35 bps INFO @ Fri, 26 Jun 2020 11:01:08: #2 alternative fragment length(s) may be 2,35,586 bps INFO @ Fri, 26 Jun 2020 11:01:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494952/SRX494952.20_model.r WARNING @ Fri, 26 Jun 2020 11:01:08: #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 11:01:08: #2 You may need to consider one of the other alternative d(s): 2,35,586 WARNING @ Fri, 26 Jun 2020 11:01:08: #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 11:01:08: #3 Call peaks... INFO @ Fri, 26 Jun 2020 11:01:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 11:01:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494952/SRX494952.05_peaks.xls INFO @ Fri, 26 Jun 2020 11:01:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494952/SRX494952.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 11:01:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494952/SRX494952.05_summits.bed INFO @ Fri, 26 Jun 2020 11:01:14: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7183 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 11:01:24: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 11:01:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494952/SRX494952.10_peaks.xls INFO @ Fri, 26 Jun 2020 11:01:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494952/SRX494952.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 11:01:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494952/SRX494952.10_summits.bed INFO @ Fri, 26 Jun 2020 11:01:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1849 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 11:01:52: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 11:02:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494952/SRX494952.20_peaks.xls INFO @ Fri, 26 Jun 2020 11:02:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494952/SRX494952.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 11:02:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494952/SRX494952.20_summits.bed INFO @ Fri, 26 Jun 2020 11:02:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (201 records, 4 fields): 1 millis CompletedMACS2peakCalling