Job ID = 6368974 SRX = SRX7971799 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:32:56 prefetch.2.10.7: 1) Downloading 'SRR11392685'... 2020-06-16T00:32:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:35:40 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:35:40 prefetch.2.10.7: 1) 'SRR11392685' was downloaded successfully 2020-06-16T00:35:40 prefetch.2.10.7: 'SRR11392685' has 0 unresolved dependencies Read 21524298 spots for SRR11392685/SRR11392685.sra Written 21524298 spots for SRR11392685/SRR11392685.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:51 21524298 reads; of these: 21524298 (100.00%) were unpaired; of these: 1194925 (5.55%) aligned 0 times 17009927 (79.03%) aligned exactly 1 time 3319446 (15.42%) aligned >1 times 94.45% overall alignment rate Time searching: 00:06:51 Overall time: 00:06:51 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] 2069553 / 20329373 = 0.1018 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 @ Tue, 16 Jun 2020 09:49:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7971799/SRX7971799.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7971799/SRX7971799.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7971799/SRX7971799.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7971799/SRX7971799.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, 16 Jun 2020 09:49:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:49:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:49:13: 1000000 INFO @ Tue, 16 Jun 2020 09:49:18: 2000000 INFO @ Tue, 16 Jun 2020 09:49:24: 3000000 INFO @ Tue, 16 Jun 2020 09:49:30: 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 @ Tue, 16 Jun 2020 09:49:35: 5000000 INFO @ Tue, 16 Jun 2020 09:49:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7971799/SRX7971799.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7971799/SRX7971799.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7971799/SRX7971799.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7971799/SRX7971799.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, 16 Jun 2020 09:49:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:49:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:49:41: 6000000 INFO @ Tue, 16 Jun 2020 09:49:43: 1000000 INFO @ Tue, 16 Jun 2020 09:49:47: 7000000 INFO @ Tue, 16 Jun 2020 09:49:49: 2000000 INFO @ Tue, 16 Jun 2020 09:49:53: 8000000 INFO @ Tue, 16 Jun 2020 09:49:55: 3000000 INFO @ Tue, 16 Jun 2020 09:49:59: 9000000 INFO @ Tue, 16 Jun 2020 09:50:01: 4000000 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 @ Tue, 16 Jun 2020 09:50:06: 10000000 INFO @ Tue, 16 Jun 2020 09:50:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7971799/SRX7971799.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7971799/SRX7971799.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7971799/SRX7971799.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7971799/SRX7971799.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, 16 Jun 2020 09:50:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:50:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:50:07: 5000000 INFO @ Tue, 16 Jun 2020 09:50:12: 11000000 INFO @ Tue, 16 Jun 2020 09:50:14: 6000000 INFO @ Tue, 16 Jun 2020 09:50:15: 1000000 INFO @ Tue, 16 Jun 2020 09:50:19: 12000000 INFO @ Tue, 16 Jun 2020 09:50:21: 7000000 INFO @ Tue, 16 Jun 2020 09:50:23: 2000000 INFO @ Tue, 16 Jun 2020 09:50:26: 13000000 INFO @ Tue, 16 Jun 2020 09:50:27: 8000000 INFO @ Tue, 16 Jun 2020 09:50:30: 3000000 INFO @ Tue, 16 Jun 2020 09:50:33: 14000000 INFO @ Tue, 16 Jun 2020 09:50:34: 9000000 INFO @ Tue, 16 Jun 2020 09:50:39: 4000000 INFO @ Tue, 16 Jun 2020 09:50:40: 15000000 INFO @ Tue, 16 Jun 2020 09:50:41: 10000000 INFO @ Tue, 16 Jun 2020 09:50:46: 5000000 INFO @ Tue, 16 Jun 2020 09:50:47: 16000000 INFO @ Tue, 16 Jun 2020 09:50:48: 11000000 INFO @ Tue, 16 Jun 2020 09:50:54: 17000000 INFO @ Tue, 16 Jun 2020 09:50:54: 6000000 INFO @ Tue, 16 Jun 2020 09:50:55: 12000000 INFO @ Tue, 16 Jun 2020 09:51:01: 18000000 INFO @ Tue, 16 Jun 2020 09:51:02: 7000000 INFO @ Tue, 16 Jun 2020 09:51:02: 13000000 INFO @ Tue, 16 Jun 2020 09:51:03: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:51:03: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:51:03: #1 total tags in treatment: 18259820 INFO @ Tue, 16 Jun 2020 09:51:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:51:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:51:03: #1 tags after filtering in treatment: 18259820 INFO @ Tue, 16 Jun 2020 09:51:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:51:03: #1 finished! INFO @ Tue, 16 Jun 2020 09:51:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:51:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:51:04: #2 number of paired peaks: 227 WARNING @ Tue, 16 Jun 2020 09:51:04: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Tue, 16 Jun 2020 09:51:04: start model_add_line... INFO @ Tue, 16 Jun 2020 09:51:04: start X-correlation... INFO @ Tue, 16 Jun 2020 09:51:04: end of X-cor INFO @ Tue, 16 Jun 2020 09:51:04: #2 finished! INFO @ Tue, 16 Jun 2020 09:51:04: #2 predicted fragment length is 74 bps INFO @ Tue, 16 Jun 2020 09:51:04: #2 alternative fragment length(s) may be 2,74 bps INFO @ Tue, 16 Jun 2020 09:51:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7971799/SRX7971799.05_model.r WARNING @ Tue, 16 Jun 2020 09:51:04: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:51:04: #2 You may need to consider one of the other alternative d(s): 2,74 WARNING @ Tue, 16 Jun 2020 09:51:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:51:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:51:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:51:09: 14000000 INFO @ Tue, 16 Jun 2020 09:51:10: 8000000 INFO @ Tue, 16 Jun 2020 09:51:15: 15000000 INFO @ Tue, 16 Jun 2020 09:51:17: 9000000 INFO @ Tue, 16 Jun 2020 09:51:22: 16000000 INFO @ Tue, 16 Jun 2020 09:51:25: 10000000 INFO @ Tue, 16 Jun 2020 09:51:29: 17000000 INFO @ Tue, 16 Jun 2020 09:51:33: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:51:35: 18000000 INFO @ Tue, 16 Jun 2020 09:51:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:51:37: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:51:37: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:51:37: #1 total tags in treatment: 18259820 INFO @ Tue, 16 Jun 2020 09:51:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:51:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:51:37: #1 tags after filtering in treatment: 18259820 INFO @ Tue, 16 Jun 2020 09:51:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:51:37: #1 finished! INFO @ Tue, 16 Jun 2020 09:51:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:51:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:51:39: #2 number of paired peaks: 227 WARNING @ Tue, 16 Jun 2020 09:51:39: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Tue, 16 Jun 2020 09:51:39: start model_add_line... INFO @ Tue, 16 Jun 2020 09:51:39: start X-correlation... INFO @ Tue, 16 Jun 2020 09:51:39: end of X-cor INFO @ Tue, 16 Jun 2020 09:51:39: #2 finished! INFO @ Tue, 16 Jun 2020 09:51:39: #2 predicted fragment length is 74 bps INFO @ Tue, 16 Jun 2020 09:51:39: #2 alternative fragment length(s) may be 2,74 bps INFO @ Tue, 16 Jun 2020 09:51:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7971799/SRX7971799.10_model.r WARNING @ Tue, 16 Jun 2020 09:51:39: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:51:39: #2 You may need to consider one of the other alternative d(s): 2,74 WARNING @ Tue, 16 Jun 2020 09:51:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:51:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:51:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:51:40: 12000000 INFO @ Tue, 16 Jun 2020 09:51:47: 13000000 INFO @ Tue, 16 Jun 2020 09:51:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7971799/SRX7971799.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:51:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7971799/SRX7971799.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:51:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7971799/SRX7971799.05_summits.bed INFO @ Tue, 16 Jun 2020 09:51:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (621 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:51:55: 14000000 INFO @ Tue, 16 Jun 2020 09:52:02: 15000000 INFO @ Tue, 16 Jun 2020 09:52:09: 16000000 INFO @ Tue, 16 Jun 2020 09:52:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:52:16: 17000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:52:23: 18000000 INFO @ Tue, 16 Jun 2020 09:52:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7971799/SRX7971799.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:52:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7971799/SRX7971799.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:52:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7971799/SRX7971799.10_summits.bed INFO @ Tue, 16 Jun 2020 09:52:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (457 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:52:25: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:52:25: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:52:25: #1 total tags in treatment: 18259820 INFO @ Tue, 16 Jun 2020 09:52:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:52:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:52:25: #1 tags after filtering in treatment: 18259820 INFO @ Tue, 16 Jun 2020 09:52:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:52:25: #1 finished! INFO @ Tue, 16 Jun 2020 09:52:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:52:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:52:27: #2 number of paired peaks: 227 WARNING @ Tue, 16 Jun 2020 09:52:27: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Tue, 16 Jun 2020 09:52:27: start model_add_line... INFO @ Tue, 16 Jun 2020 09:52:27: start X-correlation... INFO @ Tue, 16 Jun 2020 09:52:27: end of X-cor INFO @ Tue, 16 Jun 2020 09:52:27: #2 finished! INFO @ Tue, 16 Jun 2020 09:52:27: #2 predicted fragment length is 74 bps INFO @ Tue, 16 Jun 2020 09:52:27: #2 alternative fragment length(s) may be 2,74 bps INFO @ Tue, 16 Jun 2020 09:52:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7971799/SRX7971799.20_model.r WARNING @ Tue, 16 Jun 2020 09:52:27: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:52:27: #2 You may need to consider one of the other alternative d(s): 2,74 WARNING @ Tue, 16 Jun 2020 09:52:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:52:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:52:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:52:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:53:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7971799/SRX7971799.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:53:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7971799/SRX7971799.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:53:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7971799/SRX7971799.20_summits.bed INFO @ Tue, 16 Jun 2020 09:53:14: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (230 records, 4 fields): 1 millis CompletedMACS2peakCalling