Job ID = 12265134 SRX = SRX4082394 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: 00:07:27 36672575 reads; of these: 36672575 (100.00%) were unpaired; of these: 4602078 (12.55%) aligned 0 times 27935145 (76.17%) aligned exactly 1 time 4135352 (11.28%) aligned >1 times 87.45% overall alignment rate Time searching: 00:07:27 Overall time: 00:07:27 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 16 files... [bam_rmdupse_core] 18801103 / 32070497 = 0.5862 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:24:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082394/SRX4082394.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082394/SRX4082394.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082394/SRX4082394.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082394/SRX4082394.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 @ Sat, 03 Apr 2021 06:24:03: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:24:03: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:24:12: 1000000 INFO @ Sat, 03 Apr 2021 06:24:20: 2000000 INFO @ Sat, 03 Apr 2021 06:24:28: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:24:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082394/SRX4082394.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082394/SRX4082394.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082394/SRX4082394.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082394/SRX4082394.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 @ Sat, 03 Apr 2021 06:24:33: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:24:33: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:24:36: 4000000 INFO @ Sat, 03 Apr 2021 06:24:42: 1000000 INFO @ Sat, 03 Apr 2021 06:24:44: 5000000 INFO @ Sat, 03 Apr 2021 06:24:50: 2000000 INFO @ Sat, 03 Apr 2021 06:24:53: 6000000 INFO @ Sat, 03 Apr 2021 06:24:58: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:25:01: 7000000 INFO @ Sat, 03 Apr 2021 06:25:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082394/SRX4082394.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082394/SRX4082394.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082394/SRX4082394.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082394/SRX4082394.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 @ Sat, 03 Apr 2021 06:25:04: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:25:04: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:25:06: 4000000 INFO @ Sat, 03 Apr 2021 06:25:10: 8000000 INFO @ Sat, 03 Apr 2021 06:25:14: 1000000 INFO @ Sat, 03 Apr 2021 06:25:14: 5000000 INFO @ Sat, 03 Apr 2021 06:25:19: 9000000 INFO @ Sat, 03 Apr 2021 06:25:23: 6000000 INFO @ Sat, 03 Apr 2021 06:25:23: 2000000 INFO @ Sat, 03 Apr 2021 06:25:27: 10000000 INFO @ Sat, 03 Apr 2021 06:25:31: 7000000 INFO @ Sat, 03 Apr 2021 06:25:32: 3000000 INFO @ Sat, 03 Apr 2021 06:25:36: 11000000 INFO @ Sat, 03 Apr 2021 06:25:39: 8000000 INFO @ Sat, 03 Apr 2021 06:25:40: 4000000 INFO @ Sat, 03 Apr 2021 06:25:45: 12000000 INFO @ Sat, 03 Apr 2021 06:25:47: 9000000 INFO @ Sat, 03 Apr 2021 06:25:49: 5000000 INFO @ Sat, 03 Apr 2021 06:25:53: 13000000 INFO @ Sat, 03 Apr 2021 06:25:55: 10000000 INFO @ Sat, 03 Apr 2021 06:25:56: #1 tag size is determined as 48 bps INFO @ Sat, 03 Apr 2021 06:25:56: #1 tag size = 48 INFO @ Sat, 03 Apr 2021 06:25:56: #1 total tags in treatment: 13269394 INFO @ Sat, 03 Apr 2021 06:25:56: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:25:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:25:56: #1 tags after filtering in treatment: 13269394 INFO @ Sat, 03 Apr 2021 06:25:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:25:56: #1 finished! INFO @ Sat, 03 Apr 2021 06:25:56: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:25:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:25:57: #2 number of paired peaks: 1110 INFO @ Sat, 03 Apr 2021 06:25:57: start model_add_line... INFO @ Sat, 03 Apr 2021 06:25:57: start X-correlation... INFO @ Sat, 03 Apr 2021 06:25:57: end of X-cor INFO @ Sat, 03 Apr 2021 06:25:57: #2 finished! INFO @ Sat, 03 Apr 2021 06:25:57: #2 predicted fragment length is 78 bps INFO @ Sat, 03 Apr 2021 06:25:57: #2 alternative fragment length(s) may be 78 bps INFO @ Sat, 03 Apr 2021 06:25:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082394/SRX4082394.05_model.r WARNING @ Sat, 03 Apr 2021 06:25:57: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:25:57: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Sat, 03 Apr 2021 06:25:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:25:57: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:25:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:25:58: 6000000 INFO @ Sat, 03 Apr 2021 06:26:03: 11000000 INFO @ Sat, 03 Apr 2021 06:26:06: 7000000 INFO @ Sat, 03 Apr 2021 06:26:11: 12000000 INFO @ Sat, 03 Apr 2021 06:26:14: 8000000 INFO @ Sat, 03 Apr 2021 06:26:19: 13000000 INFO @ Sat, 03 Apr 2021 06:26:21: #1 tag size is determined as 48 bps INFO @ Sat, 03 Apr 2021 06:26:21: #1 tag size = 48 INFO @ Sat, 03 Apr 2021 06:26:21: #1 total tags in treatment: 13269394 INFO @ Sat, 03 Apr 2021 06:26:21: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:26:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:26:21: #1 tags after filtering in treatment: 13269394 INFO @ Sat, 03 Apr 2021 06:26:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:26:21: #1 finished! INFO @ Sat, 03 Apr 2021 06:26:21: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:26:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:26:22: 9000000 INFO @ Sat, 03 Apr 2021 06:26:23: #2 number of paired peaks: 1110 INFO @ Sat, 03 Apr 2021 06:26:23: start model_add_line... INFO @ Sat, 03 Apr 2021 06:26:23: start X-correlation... INFO @ Sat, 03 Apr 2021 06:26:23: end of X-cor INFO @ Sat, 03 Apr 2021 06:26:23: #2 finished! INFO @ Sat, 03 Apr 2021 06:26:23: #2 predicted fragment length is 78 bps INFO @ Sat, 03 Apr 2021 06:26:23: #2 alternative fragment length(s) may be 78 bps INFO @ Sat, 03 Apr 2021 06:26:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082394/SRX4082394.10_model.r WARNING @ Sat, 03 Apr 2021 06:26:23: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:26:23: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Sat, 03 Apr 2021 06:26:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:26:23: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:26:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:26:30: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:26:34: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:26:38: 11000000 INFO @ Sat, 03 Apr 2021 06:26:46: 12000000 INFO @ Sat, 03 Apr 2021 06:26:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082394/SRX4082394.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:26:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082394/SRX4082394.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:26:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082394/SRX4082394.05_summits.bed INFO @ Sat, 03 Apr 2021 06:26:53: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (16605 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:26:54: 13000000 INFO @ Sat, 03 Apr 2021 06:26:57: #1 tag size is determined as 48 bps INFO @ Sat, 03 Apr 2021 06:26:57: #1 tag size = 48 INFO @ Sat, 03 Apr 2021 06:26:57: #1 total tags in treatment: 13269394 INFO @ Sat, 03 Apr 2021 06:26:57: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:26:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:26:57: #1 tags after filtering in treatment: 13269394 INFO @ Sat, 03 Apr 2021 06:26:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:26:57: #1 finished! INFO @ Sat, 03 Apr 2021 06:26:57: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:26:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:26:58: #2 number of paired peaks: 1110 INFO @ Sat, 03 Apr 2021 06:26:58: start model_add_line... INFO @ Sat, 03 Apr 2021 06:26:58: start X-correlation... INFO @ Sat, 03 Apr 2021 06:26:58: end of X-cor INFO @ Sat, 03 Apr 2021 06:26:58: #2 finished! INFO @ Sat, 03 Apr 2021 06:26:58: #2 predicted fragment length is 78 bps INFO @ Sat, 03 Apr 2021 06:26:58: #2 alternative fragment length(s) may be 78 bps INFO @ Sat, 03 Apr 2021 06:26:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082394/SRX4082394.20_model.r WARNING @ Sat, 03 Apr 2021 06:26:58: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:26:58: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Sat, 03 Apr 2021 06:26:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:26:58: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:26:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:27:00: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:27:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082394/SRX4082394.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:27:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082394/SRX4082394.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:27:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082394/SRX4082394.10_summits.bed INFO @ Sat, 03 Apr 2021 06:27:19: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (11288 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:27:35: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:27:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082394/SRX4082394.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:27:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082394/SRX4082394.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:27:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082394/SRX4082394.20_summits.bed INFO @ Sat, 03 Apr 2021 06:27:53: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (5530 records, 4 fields): 8 millis CompletedMACS2peakCalling