Job ID = 10165653 SRX = SRX7879260 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 29480730 spots for SRR11272875/SRR11272875.sra Written 29480730 spots for SRR11272875/SRR11272875.sra fastq に変換しました。 bowtie でマッピング中... Your job 10165887 ("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: 00:06:55 29480730 reads; of these: 29480730 (100.00%) were unpaired; of these: 643102 (2.18%) aligned 0 times 24223813 (82.17%) aligned exactly 1 time 4613815 (15.65%) aligned >1 times 97.82% overall alignment rate Time searching: 00:06:55 Overall time: 00:06:55 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_rmdupse_core] 4411173 / 28837628 = 0.1530 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 19:46:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7879260/SRX7879260.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7879260/SRX7879260.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7879260/SRX7879260.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7879260/SRX7879260.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 19:46:17: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:46:17: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:46:25: 1000000 INFO @ Thu, 08 Oct 2020 19:46:32: 2000000 INFO @ Thu, 08 Oct 2020 19:46:39: 3000000 INFO @ Thu, 08 Oct 2020 19:46:45: 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 @ Thu, 08 Oct 2020 19:46:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7879260/SRX7879260.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7879260/SRX7879260.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7879260/SRX7879260.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7879260/SRX7879260.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 19:46:47: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:46:47: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:46:52: 5000000 INFO @ Thu, 08 Oct 2020 19:46:53: 1000000 INFO @ Thu, 08 Oct 2020 19:46:59: 2000000 INFO @ Thu, 08 Oct 2020 19:46:59: 6000000 INFO @ Thu, 08 Oct 2020 19:47:04: 3000000 INFO @ Thu, 08 Oct 2020 19:47:06: 7000000 INFO @ Thu, 08 Oct 2020 19:47:10: 4000000 INFO @ Thu, 08 Oct 2020 19:47:14: 8000000 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 19:47:15: 5000000 INFO @ Thu, 08 Oct 2020 19:47:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7879260/SRX7879260.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7879260/SRX7879260.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7879260/SRX7879260.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7879260/SRX7879260.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 19:47:17: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:47:17: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:47:21: 9000000 INFO @ Thu, 08 Oct 2020 19:47:21: 6000000 INFO @ Thu, 08 Oct 2020 19:47:22: 1000000 INFO @ Thu, 08 Oct 2020 19:47:27: 7000000 INFO @ Thu, 08 Oct 2020 19:47:27: 2000000 INFO @ Thu, 08 Oct 2020 19:47:28: 10000000 INFO @ Thu, 08 Oct 2020 19:47:32: 8000000 INFO @ Thu, 08 Oct 2020 19:47:32: 3000000 INFO @ Thu, 08 Oct 2020 19:47:36: 11000000 INFO @ Thu, 08 Oct 2020 19:47:37: 4000000 INFO @ Thu, 08 Oct 2020 19:47:38: 9000000 INFO @ Thu, 08 Oct 2020 19:47:43: 5000000 INFO @ Thu, 08 Oct 2020 19:47:43: 12000000 INFO @ Thu, 08 Oct 2020 19:47:44: 10000000 INFO @ Thu, 08 Oct 2020 19:47:48: 6000000 INFO @ Thu, 08 Oct 2020 19:47:49: 11000000 INFO @ Thu, 08 Oct 2020 19:47:50: 13000000 INFO @ Thu, 08 Oct 2020 19:47:53: 7000000 INFO @ Thu, 08 Oct 2020 19:47:55: 12000000 INFO @ Thu, 08 Oct 2020 19:47:57: 14000000 INFO @ Thu, 08 Oct 2020 19:47:58: 8000000 INFO @ Thu, 08 Oct 2020 19:48:00: 13000000 INFO @ Thu, 08 Oct 2020 19:48:03: 9000000 INFO @ Thu, 08 Oct 2020 19:48:04: 15000000 INFO @ Thu, 08 Oct 2020 19:48:06: 14000000 INFO @ Thu, 08 Oct 2020 19:48:08: 10000000 INFO @ Thu, 08 Oct 2020 19:48:11: 16000000 INFO @ Thu, 08 Oct 2020 19:48:12: 15000000 INFO @ Thu, 08 Oct 2020 19:48:13: 11000000 INFO @ Thu, 08 Oct 2020 19:48:17: 16000000 INFO @ Thu, 08 Oct 2020 19:48:18: 12000000 INFO @ Thu, 08 Oct 2020 19:48:19: 17000000 INFO @ Thu, 08 Oct 2020 19:48:23: 13000000 INFO @ Thu, 08 Oct 2020 19:48:23: 17000000 INFO @ Thu, 08 Oct 2020 19:48:26: 18000000 INFO @ Thu, 08 Oct 2020 19:48:28: 14000000 INFO @ Thu, 08 Oct 2020 19:48:29: 18000000 INFO @ Thu, 08 Oct 2020 19:48:33: 15000000 INFO @ Thu, 08 Oct 2020 19:48:34: 19000000 INFO @ Thu, 08 Oct 2020 19:48:35: 19000000 INFO @ Thu, 08 Oct 2020 19:48:38: 16000000 INFO @ Thu, 08 Oct 2020 19:48:41: 20000000 INFO @ Thu, 08 Oct 2020 19:48:42: 20000000 INFO @ Thu, 08 Oct 2020 19:48:43: 17000000 INFO @ Thu, 08 Oct 2020 19:48:47: 21000000 INFO @ Thu, 08 Oct 2020 19:48:48: 18000000 INFO @ Thu, 08 Oct 2020 19:48:49: 21000000 INFO @ Thu, 08 Oct 2020 19:48:53: 22000000 INFO @ Thu, 08 Oct 2020 19:48:53: 19000000 INFO @ Thu, 08 Oct 2020 19:48:56: 22000000 INFO @ Thu, 08 Oct 2020 19:48:58: 23000000 INFO @ Thu, 08 Oct 2020 19:48:58: 20000000 INFO @ Thu, 08 Oct 2020 19:49:04: 21000000 INFO @ Thu, 08 Oct 2020 19:49:04: 23000000 INFO @ Thu, 08 Oct 2020 19:49:04: 24000000 INFO @ Thu, 08 Oct 2020 19:49:06: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:49:06: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:49:06: #1 total tags in treatment: 24426455 INFO @ Thu, 08 Oct 2020 19:49:06: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:49:06: #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 19:49:07: #1 tags after filtering in treatment: 24426455 INFO @ Thu, 08 Oct 2020 19:49:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:49:07: #1 finished! INFO @ Thu, 08 Oct 2020 19:49:07: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:49:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:49:08: #2 number of paired peaks: 148 WARNING @ Thu, 08 Oct 2020 19:49:08: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Thu, 08 Oct 2020 19:49:08: start model_add_line... INFO @ Thu, 08 Oct 2020 19:49:08: start X-correlation... INFO @ Thu, 08 Oct 2020 19:49:08: end of X-cor INFO @ Thu, 08 Oct 2020 19:49:08: #2 finished! INFO @ Thu, 08 Oct 2020 19:49:08: #2 predicted fragment length is 44 bps INFO @ Thu, 08 Oct 2020 19:49:08: #2 alternative fragment length(s) may be 1,44,500,559,592 bps INFO @ Thu, 08 Oct 2020 19:49:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7879260/SRX7879260.10_model.r WARNING @ Thu, 08 Oct 2020 19:49:08: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:49:08: #2 You may need to consider one of the other alternative d(s): 1,44,500,559,592 WARNING @ Thu, 08 Oct 2020 19:49:08: #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 19:49:08: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:49:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:49:09: 22000000 INFO @ Thu, 08 Oct 2020 19:49:11: 24000000 INFO @ Thu, 08 Oct 2020 19:49:14: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 19:49:14: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:49:14: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:49:14: #1 total tags in treatment: 24426455 INFO @ Thu, 08 Oct 2020 19:49:14: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:49:14: #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 19:49:14: #1 tags after filtering in treatment: 24426455 INFO @ Thu, 08 Oct 2020 19:49:14: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:49:14: #1 finished! INFO @ Thu, 08 Oct 2020 19:49:14: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:49:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:49:16: #2 number of paired peaks: 148 WARNING @ Thu, 08 Oct 2020 19:49:16: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Thu, 08 Oct 2020 19:49:16: start model_add_line... INFO @ Thu, 08 Oct 2020 19:49:16: start X-correlation... INFO @ Thu, 08 Oct 2020 19:49:16: end of X-cor INFO @ Thu, 08 Oct 2020 19:49:16: #2 finished! INFO @ Thu, 08 Oct 2020 19:49:16: #2 predicted fragment length is 44 bps INFO @ Thu, 08 Oct 2020 19:49:16: #2 alternative fragment length(s) may be 1,44,500,559,592 bps INFO @ Thu, 08 Oct 2020 19:49:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7879260/SRX7879260.05_model.r WARNING @ Thu, 08 Oct 2020 19:49:16: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:49:16: #2 You may need to consider one of the other alternative d(s): 1,44,500,559,592 WARNING @ Thu, 08 Oct 2020 19:49:16: #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 19:49:16: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:49:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:49:19: 24000000 INFO @ Thu, 08 Oct 2020 19:49:21: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:49:21: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:49:21: #1 total tags in treatment: 24426455 INFO @ Thu, 08 Oct 2020 19:49:21: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:49:21: #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 19:49:21: #1 tags after filtering in treatment: 24426455 INFO @ Thu, 08 Oct 2020 19:49:21: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:49:21: #1 finished! INFO @ Thu, 08 Oct 2020 19:49:21: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:49:21: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:49:23: #2 number of paired peaks: 148 WARNING @ Thu, 08 Oct 2020 19:49:23: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Thu, 08 Oct 2020 19:49:23: start model_add_line... INFO @ Thu, 08 Oct 2020 19:49:23: start X-correlation... INFO @ Thu, 08 Oct 2020 19:49:23: end of X-cor INFO @ Thu, 08 Oct 2020 19:49:23: #2 finished! INFO @ Thu, 08 Oct 2020 19:49:23: #2 predicted fragment length is 44 bps INFO @ Thu, 08 Oct 2020 19:49:23: #2 alternative fragment length(s) may be 1,44,500,559,592 bps INFO @ Thu, 08 Oct 2020 19:49:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7879260/SRX7879260.20_model.r WARNING @ Thu, 08 Oct 2020 19:49:23: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:49:23: #2 You may need to consider one of the other alternative d(s): 1,44,500,559,592 WARNING @ Thu, 08 Oct 2020 19:49:23: #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 19:49:23: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:49:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:49:47: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:49:55: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:50:01: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:50:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7879260/SRX7879260.10_peaks.xls INFO @ Thu, 08 Oct 2020 19:50:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7879260/SRX7879260.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:50:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7879260/SRX7879260.10_summits.bed INFO @ Thu, 08 Oct 2020 19:50:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (446 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 19:50:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7879260/SRX7879260.05_peaks.xls INFO @ Thu, 08 Oct 2020 19:50:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7879260/SRX7879260.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:50:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7879260/SRX7879260.05_summits.bed INFO @ Thu, 08 Oct 2020 19:50:13: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (751 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:50:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7879260/SRX7879260.20_peaks.xls INFO @ Thu, 08 Oct 2020 19:50:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7879260/SRX7879260.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:50:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7879260/SRX7879260.20_summits.bed INFO @ Thu, 08 Oct 2020 19:50:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (134 records, 4 fields): 1 millis CompletedMACS2peakCalling