Job ID = 6366265 SRX = SRX1007137 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:39:51 prefetch.2.10.7: 1) Downloading 'SRR1993097'... 2020-06-15T22:39:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:42:45 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:42:45 prefetch.2.10.7: 1) 'SRR1993097' was downloaded successfully Read 37064023 spots for SRR1993097/SRR1993097.sra Written 37064023 spots for SRR1993097/SRR1993097.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: 00:05:26 37064023 reads; of these: 37064023 (100.00%) were unpaired; of these: 9959183 (26.87%) aligned 0 times 22933891 (61.88%) aligned exactly 1 time 4170949 (11.25%) aligned >1 times 73.13% overall alignment rate Time searching: 00:05:26 Overall time: 00:05:26 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] 5944189 / 27104840 = 0.2193 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 07:55:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1007137/SRX1007137.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1007137/SRX1007137.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1007137/SRX1007137.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1007137/SRX1007137.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 07:55:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:55:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:55:32: 1000000 INFO @ Tue, 16 Jun 2020 07:55:36: 2000000 INFO @ Tue, 16 Jun 2020 07:55:41: 3000000 INFO @ Tue, 16 Jun 2020 07:55:45: 4000000 INFO @ Tue, 16 Jun 2020 07:55:50: 5000000 INFO @ Tue, 16 Jun 2020 07:55:54: 6000000 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 07:55:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1007137/SRX1007137.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1007137/SRX1007137.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1007137/SRX1007137.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1007137/SRX1007137.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 07:55:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:55:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:55:59: 7000000 INFO @ Tue, 16 Jun 2020 07:56:02: 1000000 INFO @ Tue, 16 Jun 2020 07:56:03: 8000000 INFO @ Tue, 16 Jun 2020 07:56:06: 2000000 INFO @ Tue, 16 Jun 2020 07:56:08: 9000000 INFO @ Tue, 16 Jun 2020 07:56:11: 3000000 INFO @ Tue, 16 Jun 2020 07:56:12: 10000000 INFO @ Tue, 16 Jun 2020 07:56:16: 4000000 INFO @ Tue, 16 Jun 2020 07:56:17: 11000000 INFO @ Tue, 16 Jun 2020 07:56:20: 5000000 INFO @ Tue, 16 Jun 2020 07:56:22: 12000000 INFO @ Tue, 16 Jun 2020 07:56:25: 6000000 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 07:56:26: 13000000 INFO @ Tue, 16 Jun 2020 07:56:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1007137/SRX1007137.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1007137/SRX1007137.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1007137/SRX1007137.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1007137/SRX1007137.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 07:56:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:56:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:56:30: 7000000 INFO @ Tue, 16 Jun 2020 07:56:31: 14000000 INFO @ Tue, 16 Jun 2020 07:56:32: 1000000 INFO @ Tue, 16 Jun 2020 07:56:34: 8000000 INFO @ Tue, 16 Jun 2020 07:56:36: 15000000 INFO @ Tue, 16 Jun 2020 07:56:37: 2000000 INFO @ Tue, 16 Jun 2020 07:56:39: 9000000 INFO @ Tue, 16 Jun 2020 07:56:40: 16000000 INFO @ Tue, 16 Jun 2020 07:56:42: 3000000 INFO @ Tue, 16 Jun 2020 07:56:44: 10000000 INFO @ Tue, 16 Jun 2020 07:56:45: 17000000 INFO @ Tue, 16 Jun 2020 07:56:46: 4000000 INFO @ Tue, 16 Jun 2020 07:56:48: 11000000 INFO @ Tue, 16 Jun 2020 07:56:49: 18000000 INFO @ Tue, 16 Jun 2020 07:56:51: 5000000 INFO @ Tue, 16 Jun 2020 07:56:53: 12000000 INFO @ Tue, 16 Jun 2020 07:56:54: 19000000 INFO @ Tue, 16 Jun 2020 07:56:56: 6000000 INFO @ Tue, 16 Jun 2020 07:56:57: 13000000 INFO @ Tue, 16 Jun 2020 07:56:59: 20000000 INFO @ Tue, 16 Jun 2020 07:57:00: 7000000 INFO @ Tue, 16 Jun 2020 07:57:02: 14000000 INFO @ Tue, 16 Jun 2020 07:57:03: 21000000 INFO @ Tue, 16 Jun 2020 07:57:04: #1 tag size is determined as 40 bps INFO @ Tue, 16 Jun 2020 07:57:04: #1 tag size = 40 INFO @ Tue, 16 Jun 2020 07:57:04: #1 total tags in treatment: 21160651 INFO @ Tue, 16 Jun 2020 07:57:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:57:04: #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 07:57:04: #1 tags after filtering in treatment: 21160651 INFO @ Tue, 16 Jun 2020 07:57:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:57:04: #1 finished! INFO @ Tue, 16 Jun 2020 07:57:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:57:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:57:05: 8000000 INFO @ Tue, 16 Jun 2020 07:57:06: #2 number of paired peaks: 539 WARNING @ Tue, 16 Jun 2020 07:57:06: Fewer paired peaks (539) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 539 pairs to build model! INFO @ Tue, 16 Jun 2020 07:57:06: start model_add_line... INFO @ Tue, 16 Jun 2020 07:57:06: start X-correlation... INFO @ Tue, 16 Jun 2020 07:57:06: end of X-cor INFO @ Tue, 16 Jun 2020 07:57:06: #2 finished! INFO @ Tue, 16 Jun 2020 07:57:06: #2 predicted fragment length is 61 bps INFO @ Tue, 16 Jun 2020 07:57:06: #2 alternative fragment length(s) may be 3,61,74 bps INFO @ Tue, 16 Jun 2020 07:57:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1007137/SRX1007137.05_model.r WARNING @ Tue, 16 Jun 2020 07:57:06: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:57:06: #2 You may need to consider one of the other alternative d(s): 3,61,74 WARNING @ Tue, 16 Jun 2020 07:57:06: #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 07:57:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:57:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:57:07: 15000000 INFO @ Tue, 16 Jun 2020 07:57:10: 9000000 INFO @ Tue, 16 Jun 2020 07:57:11: 16000000 INFO @ Tue, 16 Jun 2020 07:57:14: 10000000 INFO @ Tue, 16 Jun 2020 07:57:16: 17000000 INFO @ Tue, 16 Jun 2020 07:57:19: 11000000 INFO @ Tue, 16 Jun 2020 07:57:20: 18000000 INFO @ Tue, 16 Jun 2020 07:57:23: 12000000 INFO @ Tue, 16 Jun 2020 07:57:25: 19000000 INFO @ Tue, 16 Jun 2020 07:57:28: 13000000 INFO @ Tue, 16 Jun 2020 07:57:30: 20000000 INFO @ Tue, 16 Jun 2020 07:57:33: 14000000 INFO @ Tue, 16 Jun 2020 07:57:34: 21000000 INFO @ Tue, 16 Jun 2020 07:57:35: #1 tag size is determined as 40 bps INFO @ Tue, 16 Jun 2020 07:57:35: #1 tag size = 40 INFO @ Tue, 16 Jun 2020 07:57:35: #1 total tags in treatment: 21160651 INFO @ Tue, 16 Jun 2020 07:57:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:57:35: #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 07:57:35: #1 tags after filtering in treatment: 21160651 INFO @ Tue, 16 Jun 2020 07:57:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:57:35: #1 finished! INFO @ Tue, 16 Jun 2020 07:57:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:57:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:57:37: #2 number of paired peaks: 539 WARNING @ Tue, 16 Jun 2020 07:57:37: Fewer paired peaks (539) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 539 pairs to build model! INFO @ Tue, 16 Jun 2020 07:57:37: start model_add_line... INFO @ Tue, 16 Jun 2020 07:57:37: start X-correlation... INFO @ Tue, 16 Jun 2020 07:57:37: end of X-cor INFO @ Tue, 16 Jun 2020 07:57:37: #2 finished! INFO @ Tue, 16 Jun 2020 07:57:37: #2 predicted fragment length is 61 bps INFO @ Tue, 16 Jun 2020 07:57:37: #2 alternative fragment length(s) may be 3,61,74 bps INFO @ Tue, 16 Jun 2020 07:57:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1007137/SRX1007137.10_model.r WARNING @ Tue, 16 Jun 2020 07:57:37: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:57:37: #2 You may need to consider one of the other alternative d(s): 3,61,74 WARNING @ Tue, 16 Jun 2020 07:57:37: #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 07:57:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:57:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:57:37: 15000000 INFO @ Tue, 16 Jun 2020 07:57:42: 16000000 INFO @ Tue, 16 Jun 2020 07:57:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:57:46: 17000000 INFO @ Tue, 16 Jun 2020 07:57:51: 18000000 INFO @ Tue, 16 Jun 2020 07:57:55: 19000000 INFO @ Tue, 16 Jun 2020 07:58:00: 20000000 INFO @ Tue, 16 Jun 2020 07:58:05: 21000000 INFO @ Tue, 16 Jun 2020 07:58:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1007137/SRX1007137.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:58:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1007137/SRX1007137.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:58:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1007137/SRX1007137.05_summits.bed INFO @ Tue, 16 Jun 2020 07:58:05: Done! INFO @ Tue, 16 Jun 2020 07:58:06: #1 tag size is determined as 40 bps INFO @ Tue, 16 Jun 2020 07:58:06: #1 tag size = 40 INFO @ Tue, 16 Jun 2020 07:58:06: #1 total tags in treatment: 21160651 INFO @ Tue, 16 Jun 2020 07:58:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:58:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (11433 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:58:06: #1 tags after filtering in treatment: 21160651 INFO @ Tue, 16 Jun 2020 07:58:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:58:06: #1 finished! INFO @ Tue, 16 Jun 2020 07:58:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:58:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:58:07: #2 number of paired peaks: 539 WARNING @ Tue, 16 Jun 2020 07:58:07: Fewer paired peaks (539) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 539 pairs to build model! INFO @ Tue, 16 Jun 2020 07:58:07: start model_add_line... INFO @ Tue, 16 Jun 2020 07:58:08: start X-correlation... INFO @ Tue, 16 Jun 2020 07:58:08: end of X-cor INFO @ Tue, 16 Jun 2020 07:58:08: #2 finished! INFO @ Tue, 16 Jun 2020 07:58:08: #2 predicted fragment length is 61 bps INFO @ Tue, 16 Jun 2020 07:58:08: #2 alternative fragment length(s) may be 3,61,74 bps INFO @ Tue, 16 Jun 2020 07:58:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1007137/SRX1007137.20_model.r WARNING @ Tue, 16 Jun 2020 07:58:08: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:58:08: #2 You may need to consider one of the other alternative d(s): 3,61,74 WARNING @ Tue, 16 Jun 2020 07:58:08: #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 07:58:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:58:08: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:58:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:58:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1007137/SRX1007137.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:58:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1007137/SRX1007137.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:58:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1007137/SRX1007137.10_summits.bed INFO @ Tue, 16 Jun 2020 07:58:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5802 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:58:48: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:59:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1007137/SRX1007137.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:59:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1007137/SRX1007137.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:59:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1007137/SRX1007137.20_summits.bed INFO @ Tue, 16 Jun 2020 07:59:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2430 records, 4 fields): 3 millis CompletedMACS2peakCalling