Job ID = 14159444 SRX = SRX3180802 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:04:51 18304315 reads; of these: 18304315 (100.00%) were unpaired; of these: 1589645 (8.68%) aligned 0 times 13338471 (72.87%) aligned exactly 1 time 3376199 (18.44%) aligned >1 times 91.32% overall alignment rate Time searching: 00:04:51 Overall time: 00:04:51 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 8 files... [bam_rmdupse_core] 4815911 / 16714670 = 0.2881 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 22:05:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180802/SRX3180802.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180802/SRX3180802.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180802/SRX3180802.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180802/SRX3180802.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 22:05:29: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:05:29: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:05:37: 1000000 INFO @ Wed, 08 Dec 2021 22:05:46: 2000000 INFO @ Wed, 08 Dec 2021 22:05:54: 3000000 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 22:05:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180802/SRX3180802.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180802/SRX3180802.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180802/SRX3180802.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180802/SRX3180802.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 22:05:58: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:05:58: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:06:02: 4000000 INFO @ Wed, 08 Dec 2021 22:06:09: 1000000 INFO @ Wed, 08 Dec 2021 22:06:11: 5000000 INFO @ Wed, 08 Dec 2021 22:06:19: 2000000 INFO @ Wed, 08 Dec 2021 22:06:19: 6000000 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 22:06:27: 7000000 INFO @ Wed, 08 Dec 2021 22:06:28: 3000000 INFO @ Wed, 08 Dec 2021 22:06:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180802/SRX3180802.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180802/SRX3180802.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180802/SRX3180802.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180802/SRX3180802.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 22:06:28: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:06:28: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:06:35: 8000000 INFO @ Wed, 08 Dec 2021 22:06:38: 4000000 INFO @ Wed, 08 Dec 2021 22:06:38: 1000000 INFO @ Wed, 08 Dec 2021 22:06:44: 9000000 INFO @ Wed, 08 Dec 2021 22:06:48: 5000000 INFO @ Wed, 08 Dec 2021 22:06:48: 2000000 INFO @ Wed, 08 Dec 2021 22:06:52: 10000000 INFO @ Wed, 08 Dec 2021 22:06:57: 3000000 INFO @ Wed, 08 Dec 2021 22:06:58: 6000000 INFO @ Wed, 08 Dec 2021 22:07:00: 11000000 INFO @ Wed, 08 Dec 2021 22:07:07: 4000000 INFO @ Wed, 08 Dec 2021 22:07:08: 7000000 INFO @ Wed, 08 Dec 2021 22:07:08: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 22:07:08: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 22:07:08: #1 total tags in treatment: 11898759 INFO @ Wed, 08 Dec 2021 22:07:08: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:07:08: #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 22:07:08: #1 tags after filtering in treatment: 11898759 INFO @ Wed, 08 Dec 2021 22:07:08: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:07:08: #1 finished! INFO @ Wed, 08 Dec 2021 22:07:08: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:07:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:07:09: #2 number of paired peaks: 457 WARNING @ Wed, 08 Dec 2021 22:07:09: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Wed, 08 Dec 2021 22:07:09: start model_add_line... INFO @ Wed, 08 Dec 2021 22:07:09: start X-correlation... INFO @ Wed, 08 Dec 2021 22:07:09: end of X-cor INFO @ Wed, 08 Dec 2021 22:07:09: #2 finished! INFO @ Wed, 08 Dec 2021 22:07:09: #2 predicted fragment length is 45 bps INFO @ Wed, 08 Dec 2021 22:07:09: #2 alternative fragment length(s) may be 2,45,545,571,598 bps INFO @ Wed, 08 Dec 2021 22:07:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180802/SRX3180802.05_model.r WARNING @ Wed, 08 Dec 2021 22:07:09: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:07:09: #2 You may need to consider one of the other alternative d(s): 2,45,545,571,598 WARNING @ Wed, 08 Dec 2021 22:07:09: #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 22:07:09: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:07:09: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:07:16: 5000000 INFO @ Wed, 08 Dec 2021 22:07:17: 8000000 INFO @ Wed, 08 Dec 2021 22:07:25: 6000000 INFO @ Wed, 08 Dec 2021 22:07:27: 9000000 INFO @ Wed, 08 Dec 2021 22:07:34: 7000000 INFO @ Wed, 08 Dec 2021 22:07:37: 10000000 INFO @ Wed, 08 Dec 2021 22:07:41: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:07:43: 8000000 INFO @ Wed, 08 Dec 2021 22:07:46: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 22:07:53: 9000000 INFO @ Wed, 08 Dec 2021 22:07:55: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 22:07:55: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 22:07:55: #1 total tags in treatment: 11898759 INFO @ Wed, 08 Dec 2021 22:07:55: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:07:55: #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 22:07:55: #1 tags after filtering in treatment: 11898759 INFO @ Wed, 08 Dec 2021 22:07:55: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:07:55: #1 finished! INFO @ Wed, 08 Dec 2021 22:07:55: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:07:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:07:56: #2 number of paired peaks: 457 WARNING @ Wed, 08 Dec 2021 22:07:56: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Wed, 08 Dec 2021 22:07:56: start model_add_line... INFO @ Wed, 08 Dec 2021 22:07:56: start X-correlation... INFO @ Wed, 08 Dec 2021 22:07:56: end of X-cor INFO @ Wed, 08 Dec 2021 22:07:56: #2 finished! INFO @ Wed, 08 Dec 2021 22:07:56: #2 predicted fragment length is 45 bps INFO @ Wed, 08 Dec 2021 22:07:56: #2 alternative fragment length(s) may be 2,45,545,571,598 bps INFO @ Wed, 08 Dec 2021 22:07:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180802/SRX3180802.10_model.r WARNING @ Wed, 08 Dec 2021 22:07:56: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:07:56: #2 You may need to consider one of the other alternative d(s): 2,45,545,571,598 WARNING @ Wed, 08 Dec 2021 22:07:56: #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 22:07:56: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:07:56: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:07:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180802/SRX3180802.05_peaks.xls INFO @ Wed, 08 Dec 2021 22:07:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180802/SRX3180802.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:07:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180802/SRX3180802.05_summits.bed INFO @ Wed, 08 Dec 2021 22:07:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (656 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:08:02: 10000000 INFO @ Wed, 08 Dec 2021 22:08:10: 11000000 INFO @ Wed, 08 Dec 2021 22:08:19: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 22:08:19: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 22:08:19: #1 total tags in treatment: 11898759 INFO @ Wed, 08 Dec 2021 22:08:19: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:08:19: #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 22:08:19: #1 tags after filtering in treatment: 11898759 INFO @ Wed, 08 Dec 2021 22:08:19: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:08:19: #1 finished! INFO @ Wed, 08 Dec 2021 22:08:19: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:08:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:08:20: #2 number of paired peaks: 457 WARNING @ Wed, 08 Dec 2021 22:08:20: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Wed, 08 Dec 2021 22:08:20: start model_add_line... INFO @ Wed, 08 Dec 2021 22:08:20: start X-correlation... INFO @ Wed, 08 Dec 2021 22:08:20: end of X-cor INFO @ Wed, 08 Dec 2021 22:08:20: #2 finished! INFO @ Wed, 08 Dec 2021 22:08:20: #2 predicted fragment length is 45 bps INFO @ Wed, 08 Dec 2021 22:08:20: #2 alternative fragment length(s) may be 2,45,545,571,598 bps INFO @ Wed, 08 Dec 2021 22:08:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180802/SRX3180802.20_model.r WARNING @ Wed, 08 Dec 2021 22:08:20: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:08:20: #2 You may need to consider one of the other alternative d(s): 2,45,545,571,598 WARNING @ Wed, 08 Dec 2021 22:08:20: #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 22:08:20: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:08:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 22:08:28: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:08:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180802/SRX3180802.10_peaks.xls INFO @ Wed, 08 Dec 2021 22:08:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180802/SRX3180802.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:08:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180802/SRX3180802.10_summits.bed INFO @ Wed, 08 Dec 2021 22:08:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (431 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:08:53: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:09:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180802/SRX3180802.20_peaks.xls INFO @ Wed, 08 Dec 2021 22:09:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180802/SRX3180802.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:09:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180802/SRX3180802.20_summits.bed INFO @ Wed, 08 Dec 2021 22:09:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (169 records, 4 fields): 2 millis CompletedMACS2peakCalling