Job ID = 10165691 SRX = SRX8832063 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 32508562 spots for SRR12332005/SRR12332005.sra Written 32508562 spots for SRR12332005/SRR12332005.sra fastq に変換しました。 bowtie でマッピング中... Your job 10165925 ("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: 00:06:31 32508562 reads; of these: 32508562 (100.00%) were unpaired; of these: 493168 (1.52%) aligned 0 times 27114447 (83.41%) aligned exactly 1 time 4900947 (15.08%) aligned >1 times 98.48% overall alignment rate Time searching: 00:06:31 Overall time: 00:06:31 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 16 files... [bam_rmdupse_core] 9732707 / 32015394 = 0.3040 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 @ Thu, 08 Oct 2020 19:51:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.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 @ Thu, 08 Oct 2020 19:51:50: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:51:50: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:51:54: 1000000 INFO @ Thu, 08 Oct 2020 19:51:59: 2000000 INFO @ Thu, 08 Oct 2020 19:52:04: 3000000 INFO @ Thu, 08 Oct 2020 19:52:09: 4000000 INFO @ Thu, 08 Oct 2020 19:52:14: 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 @ Thu, 08 Oct 2020 19:52:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.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 @ Thu, 08 Oct 2020 19:52:19: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:52:19: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:52:19: 6000000 INFO @ Thu, 08 Oct 2020 19:52:24: 1000000 INFO @ Thu, 08 Oct 2020 19:52:25: 7000000 INFO @ Thu, 08 Oct 2020 19:52:30: 2000000 INFO @ Thu, 08 Oct 2020 19:52:30: 8000000 INFO @ Thu, 08 Oct 2020 19:52:35: 3000000 INFO @ Thu, 08 Oct 2020 19:52:36: 9000000 INFO @ Thu, 08 Oct 2020 19:52:41: 4000000 INFO @ Thu, 08 Oct 2020 19:52:42: 10000000 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 @ Thu, 08 Oct 2020 19:52:47: 5000000 INFO @ Thu, 08 Oct 2020 19:52:47: 11000000 INFO @ Thu, 08 Oct 2020 19:52:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.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 @ Thu, 08 Oct 2020 19:52:49: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:52:49: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:52:53: 6000000 INFO @ Thu, 08 Oct 2020 19:52:53: 12000000 INFO @ Thu, 08 Oct 2020 19:52:54: 1000000 INFO @ Thu, 08 Oct 2020 19:52:59: 7000000 INFO @ Thu, 08 Oct 2020 19:52:59: 13000000 INFO @ Thu, 08 Oct 2020 19:53:00: 2000000 INFO @ Thu, 08 Oct 2020 19:53:05: 8000000 INFO @ Thu, 08 Oct 2020 19:53:05: 3000000 INFO @ Thu, 08 Oct 2020 19:53:05: 14000000 INFO @ Thu, 08 Oct 2020 19:53:10: 4000000 INFO @ Thu, 08 Oct 2020 19:53:11: 9000000 INFO @ Thu, 08 Oct 2020 19:53:11: 15000000 INFO @ Thu, 08 Oct 2020 19:53:15: 5000000 INFO @ Thu, 08 Oct 2020 19:53:16: 10000000 INFO @ Thu, 08 Oct 2020 19:53:17: 16000000 INFO @ Thu, 08 Oct 2020 19:53:21: 6000000 INFO @ Thu, 08 Oct 2020 19:53:22: 11000000 INFO @ Thu, 08 Oct 2020 19:53:23: 17000000 INFO @ Thu, 08 Oct 2020 19:53:26: 7000000 INFO @ Thu, 08 Oct 2020 19:53:28: 12000000 INFO @ Thu, 08 Oct 2020 19:53:29: 18000000 INFO @ Thu, 08 Oct 2020 19:53:31: 8000000 INFO @ Thu, 08 Oct 2020 19:53:34: 13000000 INFO @ Thu, 08 Oct 2020 19:53:35: 19000000 INFO @ Thu, 08 Oct 2020 19:53:36: 9000000 INFO @ Thu, 08 Oct 2020 19:53:40: 14000000 INFO @ Thu, 08 Oct 2020 19:53:41: 20000000 INFO @ Thu, 08 Oct 2020 19:53:41: 10000000 INFO @ Thu, 08 Oct 2020 19:53:46: 11000000 INFO @ Thu, 08 Oct 2020 19:53:46: 15000000 INFO @ Thu, 08 Oct 2020 19:53:47: 21000000 INFO @ Thu, 08 Oct 2020 19:53:51: 12000000 INFO @ Thu, 08 Oct 2020 19:53:52: 16000000 INFO @ Thu, 08 Oct 2020 19:53:53: 22000000 INFO @ Thu, 08 Oct 2020 19:53:55: #1 tag size is determined as 49 bps INFO @ Thu, 08 Oct 2020 19:53:55: #1 tag size = 49 INFO @ Thu, 08 Oct 2020 19:53:55: #1 total tags in treatment: 22282687 INFO @ Thu, 08 Oct 2020 19:53:55: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:53:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:53:55: #1 tags after filtering in treatment: 22282687 INFO @ Thu, 08 Oct 2020 19:53:55: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:53:55: #1 finished! INFO @ Thu, 08 Oct 2020 19:53:55: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:53:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:53:56: #2 number of paired peaks: 118 WARNING @ Thu, 08 Oct 2020 19:53:56: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Thu, 08 Oct 2020 19:53:56: start model_add_line... INFO @ Thu, 08 Oct 2020 19:53:57: 13000000 INFO @ Thu, 08 Oct 2020 19:53:57: start X-correlation... INFO @ Thu, 08 Oct 2020 19:53:57: end of X-cor INFO @ Thu, 08 Oct 2020 19:53:57: #2 finished! INFO @ Thu, 08 Oct 2020 19:53:57: #2 predicted fragment length is 47 bps INFO @ Thu, 08 Oct 2020 19:53:57: #2 alternative fragment length(s) may be 2,47,598 bps INFO @ Thu, 08 Oct 2020 19:53:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.05_model.r WARNING @ Thu, 08 Oct 2020 19:53:57: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:53:57: #2 You may need to consider one of the other alternative d(s): 2,47,598 WARNING @ Thu, 08 Oct 2020 19:53:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:53:57: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:53:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:53:58: 17000000 INFO @ Thu, 08 Oct 2020 19:54:02: 14000000 INFO @ Thu, 08 Oct 2020 19:54:03: 18000000 INFO @ Thu, 08 Oct 2020 19:54:07: 15000000 INFO @ Thu, 08 Oct 2020 19:54:09: 19000000 INFO @ Thu, 08 Oct 2020 19:54:12: 16000000 INFO @ Thu, 08 Oct 2020 19:54:14: 20000000 INFO @ Thu, 08 Oct 2020 19:54:17: 17000000 INFO @ Thu, 08 Oct 2020 19:54:19: 21000000 INFO @ Thu, 08 Oct 2020 19:54:22: 18000000 INFO @ Thu, 08 Oct 2020 19:54:24: 22000000 INFO @ Thu, 08 Oct 2020 19:54:26: #1 tag size is determined as 49 bps INFO @ Thu, 08 Oct 2020 19:54:26: #1 tag size = 49 INFO @ Thu, 08 Oct 2020 19:54:26: #1 total tags in treatment: 22282687 INFO @ Thu, 08 Oct 2020 19:54:26: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:54:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:54:26: #1 tags after filtering in treatment: 22282687 INFO @ Thu, 08 Oct 2020 19:54:26: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:54:26: #1 finished! INFO @ Thu, 08 Oct 2020 19:54:26: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:54:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:54:27: 19000000 INFO @ Thu, 08 Oct 2020 19:54:28: #2 number of paired peaks: 118 WARNING @ Thu, 08 Oct 2020 19:54:28: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Thu, 08 Oct 2020 19:54:28: start model_add_line... INFO @ Thu, 08 Oct 2020 19:54:28: start X-correlation... INFO @ Thu, 08 Oct 2020 19:54:28: end of X-cor INFO @ Thu, 08 Oct 2020 19:54:28: #2 finished! INFO @ Thu, 08 Oct 2020 19:54:28: #2 predicted fragment length is 47 bps INFO @ Thu, 08 Oct 2020 19:54:28: #2 alternative fragment length(s) may be 2,47,598 bps INFO @ Thu, 08 Oct 2020 19:54:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.10_model.r WARNING @ Thu, 08 Oct 2020 19:54:28: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:54:28: #2 You may need to consider one of the other alternative d(s): 2,47,598 WARNING @ Thu, 08 Oct 2020 19:54:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:54:28: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:54:28: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:54:31: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:54:32: 20000000 INFO @ Thu, 08 Oct 2020 19:54:37: 21000000 INFO @ Thu, 08 Oct 2020 19:54:42: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 19:54:44: #1 tag size is determined as 49 bps INFO @ Thu, 08 Oct 2020 19:54:44: #1 tag size = 49 INFO @ Thu, 08 Oct 2020 19:54:44: #1 total tags in treatment: 22282687 INFO @ Thu, 08 Oct 2020 19:54:44: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:54:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:54:44: #1 tags after filtering in treatment: 22282687 INFO @ Thu, 08 Oct 2020 19:54:44: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:54:44: #1 finished! INFO @ Thu, 08 Oct 2020 19:54:44: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:54:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:54:46: #2 number of paired peaks: 118 WARNING @ Thu, 08 Oct 2020 19:54:46: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Thu, 08 Oct 2020 19:54:46: start model_add_line... INFO @ Thu, 08 Oct 2020 19:54:46: start X-correlation... INFO @ Thu, 08 Oct 2020 19:54:46: end of X-cor INFO @ Thu, 08 Oct 2020 19:54:46: #2 finished! INFO @ Thu, 08 Oct 2020 19:54:46: #2 predicted fragment length is 47 bps INFO @ Thu, 08 Oct 2020 19:54:46: #2 alternative fragment length(s) may be 2,47,598 bps INFO @ Thu, 08 Oct 2020 19:54:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.20_model.r WARNING @ Thu, 08 Oct 2020 19:54:46: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:54:46: #2 You may need to consider one of the other alternative d(s): 2,47,598 WARNING @ Thu, 08 Oct 2020 19:54:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:54:46: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:54:46: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:54:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.05_peaks.xls INFO @ Thu, 08 Oct 2020 19:54:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:54:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.05_summits.bed INFO @ Thu, 08 Oct 2020 19:54:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4954 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:55:02: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:55:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.10_peaks.xls INFO @ Thu, 08 Oct 2020 19:55:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:55:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.10_summits.bed INFO @ Thu, 08 Oct 2020 19:55:20: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1433 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:55:21: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:55:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.20_peaks.xls INFO @ Thu, 08 Oct 2020 19:55:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:55:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.20_summits.bed INFO @ Thu, 08 Oct 2020 19:55:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (177 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。