Job ID = 14518056 SRX = SRX10533695 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 4000000 spots for SRR14165572/SRR14165572.sra Written 4000000 spots for SRR14165572/SRR14165572.sra Read 4000000 spots for SRR14165573/SRR14165573.sra Written 4000000 spots for SRR14165573/SRR14165573.sra 2022-01-14T23:10:12 prefetch.2.10.7: 1) Downloading 'SRR14165574'... 2022-01-14T23:10:12 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T23:10:22 prefetch.2.10.7: HTTPS download succeed 2022-01-14T23:10:22 prefetch.2.10.7: 'SRR14165574' is valid 2022-01-14T23:10:22 prefetch.2.10.7: 1) 'SRR14165574' was downloaded successfully 2022-01-14T23:10:22 prefetch.2.10.7: 'SRR14165574' has 0 unresolved dependencies Read 4000000 spots for SRR14165574/SRR14165574.sra Written 4000000 spots for SRR14165574/SRR14165574.sra Read 4000000 spots for SRR14165575/SRR14165575.sra Written 4000000 spots for SRR14165575/SRR14165575.sra Read 4000000 spots for SRR14165576/SRR14165576.sra Written 4000000 spots for SRR14165576/SRR14165576.sra Read 4000000 spots for SRR14165577/SRR14165577.sra Written 4000000 spots for SRR14165577/SRR14165577.sra Read 4000000 spots for SRR14165578/SRR14165578.sra Written 4000000 spots for SRR14165578/SRR14165578.sra Read 4000000 spots for SRR14165579/SRR14165579.sra Written 4000000 spots for SRR14165579/SRR14165579.sra Read 1890376 spots for SRR14165580/SRR14165580.sra Written 1890376 spots for SRR14165580/SRR14165580.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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:14:55 33890376 reads; of these: 33890376 (100.00%) were unpaired; of these: 11423567 (33.71%) aligned 0 times 16757021 (49.44%) aligned exactly 1 time 5709788 (16.85%) aligned >1 times 66.29% overall alignment rate Time searching: 00:14:58 Overall time: 00:14:58 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 1737214 / 22466809 = 0.0773 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 @ Sat, 15 Jan 2022 08:33:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX10533695/SRX10533695.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX10533695/SRX10533695.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX10533695/SRX10533695.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX10533695/SRX10533695.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 15 Jan 2022 08:33:06: #1 read tag files... INFO @ Sat, 15 Jan 2022 08:33:06: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 08:33:11: 1000000 INFO @ Sat, 15 Jan 2022 08:33:17: 2000000 INFO @ Sat, 15 Jan 2022 08:33:22: 3000000 INFO @ Sat, 15 Jan 2022 08:33:28: 4000000 INFO @ Sat, 15 Jan 2022 08:33:33: 5000000 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 @ Sat, 15 Jan 2022 08:33:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX10533695/SRX10533695.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX10533695/SRX10533695.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX10533695/SRX10533695.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX10533695/SRX10533695.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 15 Jan 2022 08:33:36: #1 read tag files... INFO @ Sat, 15 Jan 2022 08:33:36: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 08:33:39: 6000000 INFO @ Sat, 15 Jan 2022 08:33:42: 1000000 INFO @ Sat, 15 Jan 2022 08:33:45: 7000000 INFO @ Sat, 15 Jan 2022 08:33:48: 2000000 INFO @ Sat, 15 Jan 2022 08:33:51: 8000000 INFO @ Sat, 15 Jan 2022 08:33:54: 3000000 INFO @ Sat, 15 Jan 2022 08:33:57: 9000000 INFO @ Sat, 15 Jan 2022 08:34:00: 4000000 INFO @ Sat, 15 Jan 2022 08:34:04: 10000000 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 @ Sat, 15 Jan 2022 08:34:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX10533695/SRX10533695.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX10533695/SRX10533695.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX10533695/SRX10533695.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX10533695/SRX10533695.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 15 Jan 2022 08:34:06: #1 read tag files... INFO @ Sat, 15 Jan 2022 08:34:06: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 08:34:06: 5000000 INFO @ Sat, 15 Jan 2022 08:34:10: 11000000 INFO @ Sat, 15 Jan 2022 08:34:13: 6000000 INFO @ Sat, 15 Jan 2022 08:34:13: 1000000 INFO @ Sat, 15 Jan 2022 08:34:16: 12000000 INFO @ Sat, 15 Jan 2022 08:34:20: 7000000 INFO @ Sat, 15 Jan 2022 08:34:21: 2000000 INFO @ Sat, 15 Jan 2022 08:34:23: 13000000 INFO @ Sat, 15 Jan 2022 08:34:26: 8000000 INFO @ Sat, 15 Jan 2022 08:34:28: 3000000 INFO @ Sat, 15 Jan 2022 08:34:29: 14000000 INFO @ Sat, 15 Jan 2022 08:34:33: 9000000 INFO @ Sat, 15 Jan 2022 08:34:35: 4000000 INFO @ Sat, 15 Jan 2022 08:34:36: 15000000 INFO @ Sat, 15 Jan 2022 08:34:39: 10000000 INFO @ Sat, 15 Jan 2022 08:34:42: 5000000 INFO @ Sat, 15 Jan 2022 08:34:42: 16000000 INFO @ Sat, 15 Jan 2022 08:34:46: 11000000 INFO @ Sat, 15 Jan 2022 08:34:49: 17000000 INFO @ Sat, 15 Jan 2022 08:34:50: 6000000 INFO @ Sat, 15 Jan 2022 08:34:52: 12000000 INFO @ Sat, 15 Jan 2022 08:34:56: 18000000 INFO @ Sat, 15 Jan 2022 08:34:57: 7000000 INFO @ Sat, 15 Jan 2022 08:34:59: 13000000 INFO @ Sat, 15 Jan 2022 08:35:02: 19000000 INFO @ Sat, 15 Jan 2022 08:35:04: 8000000 INFO @ Sat, 15 Jan 2022 08:35:05: 14000000 INFO @ Sat, 15 Jan 2022 08:35:09: 20000000 INFO @ Sat, 15 Jan 2022 08:35:11: 9000000 INFO @ Sat, 15 Jan 2022 08:35:12: 15000000 INFO @ Sat, 15 Jan 2022 08:35:14: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 08:35:14: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 08:35:14: #1 total tags in treatment: 20729595 INFO @ Sat, 15 Jan 2022 08:35:14: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 08:35:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 08:35:14: #1 tags after filtering in treatment: 20729454 INFO @ Sat, 15 Jan 2022 08:35:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 08:35:14: #1 finished! INFO @ Sat, 15 Jan 2022 08:35:14: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 08:35:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 08:35:16: #2 number of paired peaks: 5360 INFO @ Sat, 15 Jan 2022 08:35:16: start model_add_line... INFO @ Sat, 15 Jan 2022 08:35:16: start X-correlation... INFO @ Sat, 15 Jan 2022 08:35:16: end of X-cor INFO @ Sat, 15 Jan 2022 08:35:16: #2 finished! INFO @ Sat, 15 Jan 2022 08:35:16: #2 predicted fragment length is 51 bps INFO @ Sat, 15 Jan 2022 08:35:16: #2 alternative fragment length(s) may be 51,156 bps INFO @ Sat, 15 Jan 2022 08:35:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX10533695/SRX10533695.05_model.r WARNING @ Sat, 15 Jan 2022 08:35:16: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 08:35:16: #2 You may need to consider one of the other alternative d(s): 51,156 WARNING @ Sat, 15 Jan 2022 08:35:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 08:35:16: #3 Call peaks... INFO @ Sat, 15 Jan 2022 08:35:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 08:35:18: 16000000 INFO @ Sat, 15 Jan 2022 08:35:18: 10000000 INFO @ Sat, 15 Jan 2022 08:35:25: 17000000 INFO @ Sat, 15 Jan 2022 08:35:26: 11000000 INFO @ Sat, 15 Jan 2022 08:35:32: 18000000 INFO @ Sat, 15 Jan 2022 08:35:33: 12000000 INFO @ Sat, 15 Jan 2022 08:35:38: 19000000 INFO @ Sat, 15 Jan 2022 08:35:40: 13000000 INFO @ Sat, 15 Jan 2022 08:35:45: 20000000 INFO @ Sat, 15 Jan 2022 08:35:48: 14000000 INFO @ Sat, 15 Jan 2022 08:35:50: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 08:35:50: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 08:35:50: #1 total tags in treatment: 20729595 INFO @ Sat, 15 Jan 2022 08:35:50: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 08:35:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 08:35:50: #1 tags after filtering in treatment: 20729454 INFO @ Sat, 15 Jan 2022 08:35:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 08:35:50: #1 finished! INFO @ Sat, 15 Jan 2022 08:35:50: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 08:35:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 08:35:52: #2 number of paired peaks: 5360 INFO @ Sat, 15 Jan 2022 08:35:52: start model_add_line... INFO @ Sat, 15 Jan 2022 08:35:52: start X-correlation... INFO @ Sat, 15 Jan 2022 08:35:52: end of X-cor INFO @ Sat, 15 Jan 2022 08:35:52: #2 finished! INFO @ Sat, 15 Jan 2022 08:35:52: #2 predicted fragment length is 51 bps INFO @ Sat, 15 Jan 2022 08:35:52: #2 alternative fragment length(s) may be 51,156 bps INFO @ Sat, 15 Jan 2022 08:35:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX10533695/SRX10533695.10_model.r WARNING @ Sat, 15 Jan 2022 08:35:52: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 08:35:52: #2 You may need to consider one of the other alternative d(s): 51,156 WARNING @ Sat, 15 Jan 2022 08:35:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 08:35:52: #3 Call peaks... INFO @ Sat, 15 Jan 2022 08:35:52: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 08:35:54: 15000000 INFO @ Sat, 15 Jan 2022 08:36:01: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 08:36:01: 16000000 INFO @ Sat, 15 Jan 2022 08:36:08: 17000000 INFO @ Sat, 15 Jan 2022 08:36:15: 18000000 INFO @ Sat, 15 Jan 2022 08:36:21: 19000000 INFO @ Sat, 15 Jan 2022 08:36:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX10533695/SRX10533695.05_peaks.xls INFO @ Sat, 15 Jan 2022 08:36:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX10533695/SRX10533695.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 08:36:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX10533695/SRX10533695.05_summits.bed INFO @ Sat, 15 Jan 2022 08:36:23: Done! pass1 - making usageList (66 chroms): 1 millis pass2 - checking and writing primary data (1720 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 08:36:28: 20000000 INFO @ Sat, 15 Jan 2022 08:36:33: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 08:36:33: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 08:36:33: #1 total tags in treatment: 20729595 INFO @ Sat, 15 Jan 2022 08:36:33: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 08:36:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 08:36:34: #1 tags after filtering in treatment: 20729454 INFO @ Sat, 15 Jan 2022 08:36:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 08:36:34: #1 finished! INFO @ Sat, 15 Jan 2022 08:36:34: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 08:36:34: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 08:36:36: #2 number of paired peaks: 5360 INFO @ Sat, 15 Jan 2022 08:36:36: start model_add_line... INFO @ Sat, 15 Jan 2022 08:36:36: start X-correlation... INFO @ Sat, 15 Jan 2022 08:36:36: end of X-cor INFO @ Sat, 15 Jan 2022 08:36:36: #2 finished! INFO @ Sat, 15 Jan 2022 08:36:36: #2 predicted fragment length is 51 bps INFO @ Sat, 15 Jan 2022 08:36:36: #2 alternative fragment length(s) may be 51,156 bps INFO @ Sat, 15 Jan 2022 08:36:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX10533695/SRX10533695.20_model.r WARNING @ Sat, 15 Jan 2022 08:36:36: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 08:36:36: #2 You may need to consider one of the other alternative d(s): 51,156 WARNING @ Sat, 15 Jan 2022 08:36:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 08:36:36: #3 Call peaks... INFO @ Sat, 15 Jan 2022 08:36:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 08:36:37: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 08:37:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX10533695/SRX10533695.10_peaks.xls INFO @ Sat, 15 Jan 2022 08:37:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX10533695/SRX10533695.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 08:37:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX10533695/SRX10533695.10_summits.bed INFO @ Sat, 15 Jan 2022 08:37:00: Done! pass1 - making usageList (50 chroms): 1 millis pass2 - checking and writing primary data (888 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 08:37:20: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 08:37:43: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX10533695/SRX10533695.20_peaks.xls INFO @ Sat, 15 Jan 2022 08:37:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX10533695/SRX10533695.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 08:37:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX10533695/SRX10533695.20_summits.bed INFO @ Sat, 15 Jan 2022 08:37:43: Done! pass1 - making usageList (34 chroms): 0 millis pass2 - checking and writing primary data (403 records, 4 fields): 25 millis CompletedMACS2peakCalling