Job ID = 16432796 SRX = SRX10274852 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 20318797 spots for SRR13895158/SRR13895158.sra Written 20318797 spots for SRR13895158/SRR13895158.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434096 ("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: 00:09:05 20318797 reads; of these: 20318797 (100.00%) were unpaired; of these: 603948 (2.97%) aligned 0 times 16075627 (79.12%) aligned exactly 1 time 3639222 (17.91%) aligned >1 times 97.03% overall alignment rate Time searching: 00:09:05 Overall time: 00:09:05 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] 3778754 / 19714849 = 0.1917 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 09:49:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10274852/SRX10274852.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10274852/SRX10274852.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10274852/SRX10274852.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10274852/SRX10274852.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 09:49:23: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:49:23: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:49:29: 1000000 INFO @ Tue, 02 Aug 2022 09:49:35: 2000000 INFO @ Tue, 02 Aug 2022 09:49:42: 3000000 INFO @ Tue, 02 Aug 2022 09:49:48: 4000000 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 09:49:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10274852/SRX10274852.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10274852/SRX10274852.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10274852/SRX10274852.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10274852/SRX10274852.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 09:49:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:49:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:49:56: 5000000 INFO @ Tue, 02 Aug 2022 09:50:00: 1000000 INFO @ Tue, 02 Aug 2022 09:50:05: 6000000 INFO @ Tue, 02 Aug 2022 09:50:08: 2000000 INFO @ Tue, 02 Aug 2022 09:50:13: 7000000 INFO @ Tue, 02 Aug 2022 09:50:17: 3000000 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 09:50:22: 8000000 INFO @ Tue, 02 Aug 2022 09:50:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10274852/SRX10274852.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10274852/SRX10274852.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10274852/SRX10274852.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10274852/SRX10274852.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 09:50:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:50:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:50:25: 4000000 INFO @ Tue, 02 Aug 2022 09:50:30: 1000000 INFO @ Tue, 02 Aug 2022 09:50:31: 9000000 INFO @ Tue, 02 Aug 2022 09:50:34: 5000000 INFO @ Tue, 02 Aug 2022 09:50:39: 2000000 INFO @ Tue, 02 Aug 2022 09:50:39: 10000000 INFO @ Tue, 02 Aug 2022 09:50:42: 6000000 INFO @ Tue, 02 Aug 2022 09:50:47: 3000000 INFO @ Tue, 02 Aug 2022 09:50:48: 11000000 INFO @ Tue, 02 Aug 2022 09:50:52: 7000000 INFO @ Tue, 02 Aug 2022 09:50:55: 4000000 INFO @ Tue, 02 Aug 2022 09:50:58: 12000000 INFO @ Tue, 02 Aug 2022 09:51:01: 8000000 INFO @ Tue, 02 Aug 2022 09:51:04: 5000000 INFO @ Tue, 02 Aug 2022 09:51:08: 13000000 INFO @ Tue, 02 Aug 2022 09:51:10: 9000000 INFO @ Tue, 02 Aug 2022 09:51:14: 6000000 INFO @ Tue, 02 Aug 2022 09:51:17: 14000000 INFO @ Tue, 02 Aug 2022 09:51:20: 10000000 INFO @ Tue, 02 Aug 2022 09:51:23: 7000000 INFO @ Tue, 02 Aug 2022 09:51:27: 15000000 INFO @ Tue, 02 Aug 2022 09:51:31: 8000000 INFO @ Tue, 02 Aug 2022 09:51:31: 11000000 INFO @ Tue, 02 Aug 2022 09:51:36: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 09:51:36: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 09:51:36: #1 total tags in treatment: 15936095 INFO @ Tue, 02 Aug 2022 09:51:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:51:36: #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 09:51:36: #1 tags after filtering in treatment: 15936095 INFO @ Tue, 02 Aug 2022 09:51:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:51:36: #1 finished! INFO @ Tue, 02 Aug 2022 09:51:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:51:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:51:37: #2 number of paired peaks: 369 WARNING @ Tue, 02 Aug 2022 09:51:37: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Tue, 02 Aug 2022 09:51:37: start model_add_line... INFO @ Tue, 02 Aug 2022 09:51:38: start X-correlation... INFO @ Tue, 02 Aug 2022 09:51:38: end of X-cor INFO @ Tue, 02 Aug 2022 09:51:38: #2 finished! INFO @ Tue, 02 Aug 2022 09:51:38: #2 predicted fragment length is 95 bps INFO @ Tue, 02 Aug 2022 09:51:38: #2 alternative fragment length(s) may be 4,95 bps INFO @ Tue, 02 Aug 2022 09:51:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10274852/SRX10274852.05_model.r WARNING @ Tue, 02 Aug 2022 09:51:38: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 09:51:38: #2 You may need to consider one of the other alternative d(s): 4,95 WARNING @ Tue, 02 Aug 2022 09:51:38: #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 09:51:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:51:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:51:40: 9000000 INFO @ Tue, 02 Aug 2022 09:51:41: 12000000 INFO @ Tue, 02 Aug 2022 09:51:49: 10000000 INFO @ Tue, 02 Aug 2022 09:51:51: 13000000 INFO @ Tue, 02 Aug 2022 09:51:59: 11000000 INFO @ Tue, 02 Aug 2022 09:52:00: 14000000 INFO @ Tue, 02 Aug 2022 09:52:08: 12000000 INFO @ Tue, 02 Aug 2022 09:52:10: 15000000 INFO @ Tue, 02 Aug 2022 09:52:12: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:52:17: 13000000 INFO @ Tue, 02 Aug 2022 09:52:19: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 09:52:19: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 09:52:19: #1 total tags in treatment: 15936095 INFO @ Tue, 02 Aug 2022 09:52:19: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:52:19: #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 09:52:20: #1 tags after filtering in treatment: 15936095 INFO @ Tue, 02 Aug 2022 09:52:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:52:20: #1 finished! INFO @ Tue, 02 Aug 2022 09:52:20: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:52:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:52:21: #2 number of paired peaks: 369 WARNING @ Tue, 02 Aug 2022 09:52:21: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Tue, 02 Aug 2022 09:52:21: start model_add_line... INFO @ Tue, 02 Aug 2022 09:52:21: start X-correlation... INFO @ Tue, 02 Aug 2022 09:52:21: end of X-cor INFO @ Tue, 02 Aug 2022 09:52:21: #2 finished! INFO @ Tue, 02 Aug 2022 09:52:21: #2 predicted fragment length is 95 bps INFO @ Tue, 02 Aug 2022 09:52:21: #2 alternative fragment length(s) may be 4,95 bps INFO @ Tue, 02 Aug 2022 09:52:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10274852/SRX10274852.10_model.r WARNING @ Tue, 02 Aug 2022 09:52:21: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 09:52:21: #2 You may need to consider one of the other alternative d(s): 4,95 WARNING @ Tue, 02 Aug 2022 09:52:21: #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 09:52:21: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:52:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:52:25: 14000000 INFO @ Tue, 02 Aug 2022 09:52:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10274852/SRX10274852.05_peaks.xls INFO @ Tue, 02 Aug 2022 09:52:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10274852/SRX10274852.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:52:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10274852/SRX10274852.05_summits.bed INFO @ Tue, 02 Aug 2022 09:52:30: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (11454 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:52:34: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 09:52:43: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 09:52:43: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 09:52:43: #1 total tags in treatment: 15936095 INFO @ Tue, 02 Aug 2022 09:52:43: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:52:43: #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 09:52:43: #1 tags after filtering in treatment: 15936095 INFO @ Tue, 02 Aug 2022 09:52:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:52:43: #1 finished! INFO @ Tue, 02 Aug 2022 09:52:43: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:52:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:52:44: #2 number of paired peaks: 369 WARNING @ Tue, 02 Aug 2022 09:52:44: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Tue, 02 Aug 2022 09:52:44: start model_add_line... INFO @ Tue, 02 Aug 2022 09:52:44: start X-correlation... INFO @ Tue, 02 Aug 2022 09:52:44: end of X-cor INFO @ Tue, 02 Aug 2022 09:52:44: #2 finished! INFO @ Tue, 02 Aug 2022 09:52:44: #2 predicted fragment length is 95 bps INFO @ Tue, 02 Aug 2022 09:52:44: #2 alternative fragment length(s) may be 4,95 bps INFO @ Tue, 02 Aug 2022 09:52:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10274852/SRX10274852.20_model.r WARNING @ Tue, 02 Aug 2022 09:52:44: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 09:52:44: #2 You may need to consider one of the other alternative d(s): 4,95 WARNING @ Tue, 02 Aug 2022 09:52:44: #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 09:52:44: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:52:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:52:53: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:53:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10274852/SRX10274852.10_peaks.xls INFO @ Tue, 02 Aug 2022 09:53:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10274852/SRX10274852.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:53:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10274852/SRX10274852.10_summits.bed INFO @ Tue, 02 Aug 2022 09:53:09: Done! pass1 - making usageList (6 chroms): 4 millis pass2 - checking and writing primary data (4531 records, 4 fields): 48 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:53:18: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 09:53:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10274852/SRX10274852.20_peaks.xls INFO @ Tue, 02 Aug 2022 09:53:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10274852/SRX10274852.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:53:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10274852/SRX10274852.20_summits.bed INFO @ Tue, 02 Aug 2022 09:53:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1137 records, 4 fields): 15 millis CompletedMACS2peakCalling