Job ID = 14158253 SRX = SRX7739521 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 17240034 spots for SRR11100925/SRR11100925.sra Written 17240034 spots for SRR11100925/SRR11100925.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158769 ("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: 00:03:57 17240034 reads; of these: 17240034 (100.00%) were unpaired; of these: 2456961 (14.25%) aligned 0 times 12280074 (71.23%) aligned exactly 1 time 2502999 (14.52%) aligned >1 times 85.75% overall alignment rate Time searching: 00:03:57 Overall time: 00:03:57 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] 1546236 / 14783073 = 0.1046 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 15:31:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7739521/SRX7739521.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7739521/SRX7739521.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7739521/SRX7739521.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7739521/SRX7739521.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 @ Wed, 08 Dec 2021 15:31:07: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:31:07: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:31:17: 1000000 INFO @ Wed, 08 Dec 2021 15:31:26: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 15:31:36: 3000000 INFO @ Wed, 08 Dec 2021 15:31:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7739521/SRX7739521.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7739521/SRX7739521.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7739521/SRX7739521.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7739521/SRX7739521.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 @ Wed, 08 Dec 2021 15:31:37: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:31:37: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:31:46: 4000000 INFO @ Wed, 08 Dec 2021 15:31:48: 1000000 INFO @ Wed, 08 Dec 2021 15:31:56: 5000000 INFO @ Wed, 08 Dec 2021 15:31:57: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 15:32:06: 6000000 INFO @ Wed, 08 Dec 2021 15:32:07: 3000000 INFO @ Wed, 08 Dec 2021 15:32:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7739521/SRX7739521.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7739521/SRX7739521.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7739521/SRX7739521.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7739521/SRX7739521.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 @ Wed, 08 Dec 2021 15:32:07: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:32:07: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:32:16: 7000000 INFO @ Wed, 08 Dec 2021 15:32:17: 4000000 INFO @ Wed, 08 Dec 2021 15:32:19: 1000000 INFO @ Wed, 08 Dec 2021 15:32:25: 8000000 INFO @ Wed, 08 Dec 2021 15:32:28: 5000000 INFO @ Wed, 08 Dec 2021 15:32:30: 2000000 INFO @ Wed, 08 Dec 2021 15:32:35: 9000000 INFO @ Wed, 08 Dec 2021 15:32:39: 6000000 INFO @ Wed, 08 Dec 2021 15:32:42: 3000000 INFO @ Wed, 08 Dec 2021 15:32:45: 10000000 INFO @ Wed, 08 Dec 2021 15:32:50: 7000000 INFO @ Wed, 08 Dec 2021 15:32:53: 4000000 INFO @ Wed, 08 Dec 2021 15:32:55: 11000000 INFO @ Wed, 08 Dec 2021 15:33:01: 8000000 INFO @ Wed, 08 Dec 2021 15:33:03: 5000000 INFO @ Wed, 08 Dec 2021 15:33:04: 12000000 INFO @ Wed, 08 Dec 2021 15:33:13: 9000000 INFO @ Wed, 08 Dec 2021 15:33:14: 13000000 INFO @ Wed, 08 Dec 2021 15:33:14: 6000000 INFO @ Wed, 08 Dec 2021 15:33:16: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 15:33:16: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 15:33:16: #1 total tags in treatment: 13236837 INFO @ Wed, 08 Dec 2021 15:33:16: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:33:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 15:33:16: #1 tags after filtering in treatment: 13236837 INFO @ Wed, 08 Dec 2021 15:33:16: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 15:33:16: #1 finished! INFO @ Wed, 08 Dec 2021 15:33:16: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:33:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:33:17: #2 number of paired peaks: 328 WARNING @ Wed, 08 Dec 2021 15:33:17: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Wed, 08 Dec 2021 15:33:17: start model_add_line... INFO @ Wed, 08 Dec 2021 15:33:18: start X-correlation... INFO @ Wed, 08 Dec 2021 15:33:18: end of X-cor INFO @ Wed, 08 Dec 2021 15:33:18: #2 finished! INFO @ Wed, 08 Dec 2021 15:33:18: #2 predicted fragment length is 50 bps INFO @ Wed, 08 Dec 2021 15:33:18: #2 alternative fragment length(s) may be 2,50 bps INFO @ Wed, 08 Dec 2021 15:33:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7739521/SRX7739521.05_model.r WARNING @ Wed, 08 Dec 2021 15:33:18: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 15:33:18: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Wed, 08 Dec 2021 15:33:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 15:33:18: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:33:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:33:23: 10000000 INFO @ Wed, 08 Dec 2021 15:33:26: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 15:33:34: 11000000 INFO @ Wed, 08 Dec 2021 15:33:36: 8000000 INFO @ Wed, 08 Dec 2021 15:33:45: 12000000 INFO @ Wed, 08 Dec 2021 15:33:48: 9000000 INFO @ Wed, 08 Dec 2021 15:33:51: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:33:56: 13000000 INFO @ Wed, 08 Dec 2021 15:33:58: 10000000 INFO @ Wed, 08 Dec 2021 15:33:58: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 15:33:58: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 15:33:58: #1 total tags in treatment: 13236837 INFO @ Wed, 08 Dec 2021 15:33:58: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:33:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 15:33:59: #1 tags after filtering in treatment: 13236837 INFO @ Wed, 08 Dec 2021 15:33:59: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 15:33:59: #1 finished! INFO @ Wed, 08 Dec 2021 15:33:59: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:33:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:34:00: #2 number of paired peaks: 328 WARNING @ Wed, 08 Dec 2021 15:34:00: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Wed, 08 Dec 2021 15:34:00: start model_add_line... INFO @ Wed, 08 Dec 2021 15:34:00: start X-correlation... INFO @ Wed, 08 Dec 2021 15:34:00: end of X-cor INFO @ Wed, 08 Dec 2021 15:34:00: #2 finished! INFO @ Wed, 08 Dec 2021 15:34:00: #2 predicted fragment length is 50 bps INFO @ Wed, 08 Dec 2021 15:34:00: #2 alternative fragment length(s) may be 2,50 bps INFO @ Wed, 08 Dec 2021 15:34:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7739521/SRX7739521.10_model.r WARNING @ Wed, 08 Dec 2021 15:34:00: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 15:34:00: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Wed, 08 Dec 2021 15:34:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 15:34:00: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:34:00: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:34:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7739521/SRX7739521.05_peaks.xls INFO @ Wed, 08 Dec 2021 15:34:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7739521/SRX7739521.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:34:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7739521/SRX7739521.05_summits.bed INFO @ Wed, 08 Dec 2021 15:34:08: Done! INFO @ Wed, 08 Dec 2021 15:34:08: 11000000 pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (674 records, 4 fields): 11 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 15:34:17: 12000000 INFO @ Wed, 08 Dec 2021 15:34:26: 13000000 INFO @ Wed, 08 Dec 2021 15:34:28: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 15:34:28: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 15:34:28: #1 total tags in treatment: 13236837 INFO @ Wed, 08 Dec 2021 15:34:28: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:34:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 15:34:28: #1 tags after filtering in treatment: 13236837 INFO @ Wed, 08 Dec 2021 15:34:28: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 15:34:28: #1 finished! INFO @ Wed, 08 Dec 2021 15:34:28: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:34:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:34:29: #2 number of paired peaks: 328 WARNING @ Wed, 08 Dec 2021 15:34:29: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Wed, 08 Dec 2021 15:34:29: start model_add_line... INFO @ Wed, 08 Dec 2021 15:34:29: start X-correlation... INFO @ Wed, 08 Dec 2021 15:34:29: end of X-cor INFO @ Wed, 08 Dec 2021 15:34:29: #2 finished! INFO @ Wed, 08 Dec 2021 15:34:29: #2 predicted fragment length is 50 bps INFO @ Wed, 08 Dec 2021 15:34:29: #2 alternative fragment length(s) may be 2,50 bps INFO @ Wed, 08 Dec 2021 15:34:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7739521/SRX7739521.20_model.r WARNING @ Wed, 08 Dec 2021 15:34:29: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 15:34:29: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Wed, 08 Dec 2021 15:34:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 15:34:29: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:34:29: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:34:34: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:34:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7739521/SRX7739521.10_peaks.xls INFO @ Wed, 08 Dec 2021 15:34:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7739521/SRX7739521.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:34:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7739521/SRX7739521.10_summits.bed INFO @ Wed, 08 Dec 2021 15:34:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (491 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:35:03: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:35:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7739521/SRX7739521.20_peaks.xls INFO @ Wed, 08 Dec 2021 15:35:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7739521/SRX7739521.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:35:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7739521/SRX7739521.20_summits.bed INFO @ Wed, 08 Dec 2021 15:35:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (193 records, 4 fields): 1 millis CompletedMACS2peakCalling