Job ID = 16434853 SRX = SRX10435522 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 19737524 spots for SRR14060922/SRR14060922.sra Written 19737524 spots for SRR14060922/SRR14060922.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434903 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:24 19737524 reads; of these: 19737524 (100.00%) were unpaired; of these: 5701548 (28.89%) aligned 0 times 11851382 (60.04%) aligned exactly 1 time 2184594 (11.07%) aligned >1 times 71.11% overall alignment rate Time searching: 00:06:25 Overall time: 00:06:25 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] 1523320 / 14035976 = 0.1085 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:15:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435522/SRX10435522.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435522/SRX10435522.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435522/SRX10435522.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435522/SRX10435522.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 @ Tue, 02 Aug 2022 10:15:04: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:15:04: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:15:14: 1000000 INFO @ Tue, 02 Aug 2022 10:15:25: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:15:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435522/SRX10435522.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435522/SRX10435522.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435522/SRX10435522.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435522/SRX10435522.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 @ Tue, 02 Aug 2022 10:15:32: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:15:32: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:15:33: 3000000 INFO @ Tue, 02 Aug 2022 10:15:42: 1000000 INFO @ Tue, 02 Aug 2022 10:15:42: 4000000 INFO @ Tue, 02 Aug 2022 10:15:50: 5000000 INFO @ Tue, 02 Aug 2022 10:15:51: 2000000 INFO @ Tue, 02 Aug 2022 10:15:58: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:16:00: 3000000 INFO @ Tue, 02 Aug 2022 10:16:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435522/SRX10435522.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435522/SRX10435522.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435522/SRX10435522.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435522/SRX10435522.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 @ Tue, 02 Aug 2022 10:16:03: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:16:03: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:16:06: 7000000 INFO @ Tue, 02 Aug 2022 10:16:09: 4000000 INFO @ Tue, 02 Aug 2022 10:16:13: 1000000 INFO @ Tue, 02 Aug 2022 10:16:14: 8000000 INFO @ Tue, 02 Aug 2022 10:16:18: 5000000 INFO @ Tue, 02 Aug 2022 10:16:22: 2000000 INFO @ Tue, 02 Aug 2022 10:16:22: 9000000 INFO @ Tue, 02 Aug 2022 10:16:27: 6000000 INFO @ Tue, 02 Aug 2022 10:16:29: 10000000 INFO @ Tue, 02 Aug 2022 10:16:30: 3000000 INFO @ Tue, 02 Aug 2022 10:16:36: 7000000 INFO @ Tue, 02 Aug 2022 10:16:37: 11000000 INFO @ Tue, 02 Aug 2022 10:16:39: 4000000 INFO @ Tue, 02 Aug 2022 10:16:45: 8000000 INFO @ Tue, 02 Aug 2022 10:16:44: 12000000 INFO @ Tue, 02 Aug 2022 10:16:48: 5000000 INFO @ Tue, 02 Aug 2022 10:16:48: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:16:48: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:16:48: #1 total tags in treatment: 12512656 INFO @ Tue, 02 Aug 2022 10:16:48: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:16:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:16:49: #1 tags after filtering in treatment: 12512656 INFO @ Tue, 02 Aug 2022 10:16:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:16:49: #1 finished! INFO @ Tue, 02 Aug 2022 10:16:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:16:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:16:50: #2 number of paired peaks: 386 WARNING @ Tue, 02 Aug 2022 10:16:50: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Tue, 02 Aug 2022 10:16:50: start model_add_line... INFO @ Tue, 02 Aug 2022 10:16:50: start X-correlation... INFO @ Tue, 02 Aug 2022 10:16:50: end of X-cor INFO @ Tue, 02 Aug 2022 10:16:50: #2 finished! INFO @ Tue, 02 Aug 2022 10:16:50: #2 predicted fragment length is 98 bps INFO @ Tue, 02 Aug 2022 10:16:50: #2 alternative fragment length(s) may be 98 bps INFO @ Tue, 02 Aug 2022 10:16:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435522/SRX10435522.05_model.r WARNING @ Tue, 02 Aug 2022 10:16:50: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:16:50: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Tue, 02 Aug 2022 10:16:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:16:50: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:16:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:16:53: 9000000 INFO @ Tue, 02 Aug 2022 10:16:55: 6000000 INFO @ Tue, 02 Aug 2022 10:17:01: 10000000 INFO @ Tue, 02 Aug 2022 10:17:03: 7000000 INFO @ Tue, 02 Aug 2022 10:17:09: 11000000 INFO @ Tue, 02 Aug 2022 10:17:11: 8000000 INFO @ Tue, 02 Aug 2022 10:17:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:17:17: 12000000 INFO @ Tue, 02 Aug 2022 10:17:18: 9000000 INFO @ Tue, 02 Aug 2022 10:17:21: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:17:21: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:17:21: #1 total tags in treatment: 12512656 INFO @ Tue, 02 Aug 2022 10:17:21: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:17:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:17:21: #1 tags after filtering in treatment: 12512656 INFO @ Tue, 02 Aug 2022 10:17:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:17:21: #1 finished! INFO @ Tue, 02 Aug 2022 10:17:21: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:17:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:17:22: #2 number of paired peaks: 386 WARNING @ Tue, 02 Aug 2022 10:17:22: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Tue, 02 Aug 2022 10:17:22: start model_add_line... INFO @ Tue, 02 Aug 2022 10:17:22: start X-correlation... INFO @ Tue, 02 Aug 2022 10:17:23: end of X-cor INFO @ Tue, 02 Aug 2022 10:17:23: #2 finished! INFO @ Tue, 02 Aug 2022 10:17:23: #2 predicted fragment length is 98 bps INFO @ Tue, 02 Aug 2022 10:17:23: #2 alternative fragment length(s) may be 98 bps INFO @ Tue, 02 Aug 2022 10:17:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435522/SRX10435522.10_model.r WARNING @ Tue, 02 Aug 2022 10:17:23: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:17:23: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Tue, 02 Aug 2022 10:17:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:17:23: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:17:23: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:17:26: 10000000 INFO @ Tue, 02 Aug 2022 10:17:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435522/SRX10435522.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:17:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435522/SRX10435522.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:17:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435522/SRX10435522.05_summits.bed INFO @ Tue, 02 Aug 2022 10:17:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1651 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:17:32: 11000000 INFO @ Tue, 02 Aug 2022 10:17:39: 12000000 INFO @ Tue, 02 Aug 2022 10:17:43: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:17:43: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:17:43: #1 total tags in treatment: 12512656 INFO @ Tue, 02 Aug 2022 10:17:43: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:17:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:17:43: #1 tags after filtering in treatment: 12512656 INFO @ Tue, 02 Aug 2022 10:17:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:17:43: #1 finished! INFO @ Tue, 02 Aug 2022 10:17:43: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:17:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:17:44: #2 number of paired peaks: 386 WARNING @ Tue, 02 Aug 2022 10:17:44: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Tue, 02 Aug 2022 10:17:44: start model_add_line... INFO @ Tue, 02 Aug 2022 10:17:44: start X-correlation... INFO @ Tue, 02 Aug 2022 10:17:45: end of X-cor INFO @ Tue, 02 Aug 2022 10:17:45: #2 finished! INFO @ Tue, 02 Aug 2022 10:17:45: #2 predicted fragment length is 98 bps INFO @ Tue, 02 Aug 2022 10:17:45: #2 alternative fragment length(s) may be 98 bps INFO @ Tue, 02 Aug 2022 10:17:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435522/SRX10435522.20_model.r WARNING @ Tue, 02 Aug 2022 10:17:45: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:17:45: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Tue, 02 Aug 2022 10:17:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:17:45: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:17:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:17:49: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:18:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435522/SRX10435522.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:18:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435522/SRX10435522.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:18:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435522/SRX10435522.10_summits.bed INFO @ Tue, 02 Aug 2022 10:18:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1107 records, 4 fields): 21 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:18:11: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:18:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435522/SRX10435522.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:18:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435522/SRX10435522.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:18:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435522/SRX10435522.20_summits.bed INFO @ Tue, 02 Aug 2022 10:18:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (632 records, 4 fields): 16 millis CompletedMACS2peakCalling