Job ID = 12264750 SRX = SRX2333003 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 49739109 spots for SRR5000683/SRR5000683.sra Written 49739109 spots for SRR5000683/SRR5000683.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265441 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:35:51 49739109 reads; of these: 49739109 (100.00%) were paired; of these: 39325083 (79.06%) aligned concordantly 0 times 8719155 (17.53%) aligned concordantly exactly 1 time 1694871 (3.41%) aligned concordantly >1 times ---- 39325083 pairs aligned concordantly 0 times; of these: 2542533 (6.47%) aligned discordantly 1 time ---- 36782550 pairs aligned 0 times concordantly or discordantly; of these: 73565100 mates make up the pairs; of these: 72352589 (98.35%) aligned 0 times 457062 (0.62%) aligned exactly 1 time 755449 (1.03%) aligned >1 times 27.27% overall alignment rate Time searching: 00:35:52 Overall time: 00:35:52 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 2658286 / 12877386 = 0.2064 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 06:51:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2333003/SRX2333003.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2333003/SRX2333003.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2333003/SRX2333003.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2333003/SRX2333003.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 06:51:37: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:51:37: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:51:45: 1000000 INFO @ Sat, 03 Apr 2021 06:51:53: 2000000 INFO @ Sat, 03 Apr 2021 06:52:01: 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 06:52:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2333003/SRX2333003.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2333003/SRX2333003.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2333003/SRX2333003.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2333003/SRX2333003.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 06:52:07: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:52:07: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:52:09: 4000000 INFO @ Sat, 03 Apr 2021 06:52:16: 1000000 INFO @ Sat, 03 Apr 2021 06:52:18: 5000000 INFO @ Sat, 03 Apr 2021 06:52:25: 2000000 INFO @ Sat, 03 Apr 2021 06:52:27: 6000000 INFO @ Sat, 03 Apr 2021 06:52:34: 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 06:52:35: 7000000 INFO @ Sat, 03 Apr 2021 06:52:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2333003/SRX2333003.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2333003/SRX2333003.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2333003/SRX2333003.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2333003/SRX2333003.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 06:52:37: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:52:37: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:52:43: 4000000 INFO @ Sat, 03 Apr 2021 06:52:44: 8000000 INFO @ Sat, 03 Apr 2021 06:52:46: 1000000 INFO @ Sat, 03 Apr 2021 06:52:52: 5000000 INFO @ Sat, 03 Apr 2021 06:52:53: 9000000 INFO @ Sat, 03 Apr 2021 06:52:56: 2000000 INFO @ Sat, 03 Apr 2021 06:53:01: 6000000 INFO @ Sat, 03 Apr 2021 06:53:02: 10000000 INFO @ Sat, 03 Apr 2021 06:53:05: 3000000 INFO @ Sat, 03 Apr 2021 06:53:10: 7000000 INFO @ Sat, 03 Apr 2021 06:53:11: 11000000 INFO @ Sat, 03 Apr 2021 06:53:14: 4000000 INFO @ Sat, 03 Apr 2021 06:53:19: 8000000 INFO @ Sat, 03 Apr 2021 06:53:20: 12000000 INFO @ Sat, 03 Apr 2021 06:53:23: 5000000 INFO @ Sat, 03 Apr 2021 06:53:28: 9000000 INFO @ Sat, 03 Apr 2021 06:53:29: 13000000 INFO @ Sat, 03 Apr 2021 06:53:33: 6000000 INFO @ Sat, 03 Apr 2021 06:53:37: 10000000 INFO @ Sat, 03 Apr 2021 06:53:38: 14000000 INFO @ Sat, 03 Apr 2021 06:53:41: 7000000 INFO @ Sat, 03 Apr 2021 06:53:46: 11000000 INFO @ Sat, 03 Apr 2021 06:53:47: 15000000 INFO @ Sat, 03 Apr 2021 06:53:51: 8000000 INFO @ Sat, 03 Apr 2021 06:53:55: 12000000 INFO @ Sat, 03 Apr 2021 06:53:56: 16000000 INFO @ Sat, 03 Apr 2021 06:54:00: 9000000 INFO @ Sat, 03 Apr 2021 06:54:04: 13000000 INFO @ Sat, 03 Apr 2021 06:54:05: 17000000 INFO @ Sat, 03 Apr 2021 06:54:09: 10000000 INFO @ Sat, 03 Apr 2021 06:54:13: 14000000 INFO @ Sat, 03 Apr 2021 06:54:14: 18000000 INFO @ Sat, 03 Apr 2021 06:54:17: 11000000 INFO @ Sat, 03 Apr 2021 06:54:22: 15000000 INFO @ Sat, 03 Apr 2021 06:54:23: 19000000 INFO @ Sat, 03 Apr 2021 06:54:26: 12000000 INFO @ Sat, 03 Apr 2021 06:54:30: 16000000 INFO @ Sat, 03 Apr 2021 06:54:33: 20000000 INFO @ Sat, 03 Apr 2021 06:54:35: 13000000 INFO @ Sat, 03 Apr 2021 06:54:39: 17000000 INFO @ Sat, 03 Apr 2021 06:54:43: 21000000 INFO @ Sat, 03 Apr 2021 06:54:44: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:54:48: 18000000 INFO @ Sat, 03 Apr 2021 06:54:50: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 06:54:50: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 06:54:50: #1 total tags in treatment: 8165678 INFO @ Sat, 03 Apr 2021 06:54:50: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:54:50: #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 06:54:51: #1 tags after filtering in treatment: 6011708 INFO @ Sat, 03 Apr 2021 06:54:51: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 06:54:51: #1 finished! INFO @ Sat, 03 Apr 2021 06:54:51: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:54:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:54:51: #2 number of paired peaks: 418 WARNING @ Sat, 03 Apr 2021 06:54:51: Fewer paired peaks (418) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 418 pairs to build model! INFO @ Sat, 03 Apr 2021 06:54:51: start model_add_line... INFO @ Sat, 03 Apr 2021 06:54:51: start X-correlation... INFO @ Sat, 03 Apr 2021 06:54:51: end of X-cor INFO @ Sat, 03 Apr 2021 06:54:51: #2 finished! INFO @ Sat, 03 Apr 2021 06:54:51: #2 predicted fragment length is 150 bps INFO @ Sat, 03 Apr 2021 06:54:51: #2 alternative fragment length(s) may be 150 bps INFO @ Sat, 03 Apr 2021 06:54:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2333003/SRX2333003.05_model.r WARNING @ Sat, 03 Apr 2021 06:54:51: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:54:51: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Sat, 03 Apr 2021 06:54:51: #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 06:54:51: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:54:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:54:52: 15000000 INFO @ Sat, 03 Apr 2021 06:54:57: 19000000 INFO @ Sat, 03 Apr 2021 06:55:01: 16000000 INFO @ Sat, 03 Apr 2021 06:55:04: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:55:06: 20000000 INFO @ Sat, 03 Apr 2021 06:55:09: 17000000 INFO @ Sat, 03 Apr 2021 06:55:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2333003/SRX2333003.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:55:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2333003/SRX2333003.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:55:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2333003/SRX2333003.05_summits.bed INFO @ Sat, 03 Apr 2021 06:55:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2763 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:55:15: 21000000 INFO @ Sat, 03 Apr 2021 06:55:18: 18000000 INFO @ Sat, 03 Apr 2021 06:55:22: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 06:55:22: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 06:55:22: #1 total tags in treatment: 8165678 INFO @ Sat, 03 Apr 2021 06:55:22: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:55:22: #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 06:55:22: #1 tags after filtering in treatment: 6011708 INFO @ Sat, 03 Apr 2021 06:55:22: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 06:55:22: #1 finished! INFO @ Sat, 03 Apr 2021 06:55:22: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:55:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:55:23: #2 number of paired peaks: 418 WARNING @ Sat, 03 Apr 2021 06:55:23: Fewer paired peaks (418) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 418 pairs to build model! INFO @ Sat, 03 Apr 2021 06:55:23: start model_add_line... INFO @ Sat, 03 Apr 2021 06:55:23: start X-correlation... INFO @ Sat, 03 Apr 2021 06:55:23: end of X-cor INFO @ Sat, 03 Apr 2021 06:55:23: #2 finished! INFO @ Sat, 03 Apr 2021 06:55:23: #2 predicted fragment length is 150 bps INFO @ Sat, 03 Apr 2021 06:55:23: #2 alternative fragment length(s) may be 150 bps INFO @ Sat, 03 Apr 2021 06:55:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2333003/SRX2333003.10_model.r WARNING @ Sat, 03 Apr 2021 06:55:23: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:55:23: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Sat, 03 Apr 2021 06:55:23: #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 06:55:23: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:55:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:55:26: 19000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:55:34: 20000000 INFO @ Sat, 03 Apr 2021 06:55:36: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:55:42: 21000000 INFO @ Sat, 03 Apr 2021 06:55:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2333003/SRX2333003.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:55:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2333003/SRX2333003.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:55:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2333003/SRX2333003.10_summits.bed INFO @ Sat, 03 Apr 2021 06:55:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1255 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:55:49: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 06:55:49: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 06:55:49: #1 total tags in treatment: 8165678 INFO @ Sat, 03 Apr 2021 06:55:49: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:55:49: #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 06:55:49: #1 tags after filtering in treatment: 6011708 INFO @ Sat, 03 Apr 2021 06:55:49: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 06:55:49: #1 finished! INFO @ Sat, 03 Apr 2021 06:55:49: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:55:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:55:49: #2 number of paired peaks: 418 WARNING @ Sat, 03 Apr 2021 06:55:49: Fewer paired peaks (418) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 418 pairs to build model! INFO @ Sat, 03 Apr 2021 06:55:49: start model_add_line... INFO @ Sat, 03 Apr 2021 06:55:49: start X-correlation... INFO @ Sat, 03 Apr 2021 06:55:49: end of X-cor INFO @ Sat, 03 Apr 2021 06:55:49: #2 finished! INFO @ Sat, 03 Apr 2021 06:55:49: #2 predicted fragment length is 150 bps INFO @ Sat, 03 Apr 2021 06:55:49: #2 alternative fragment length(s) may be 150 bps INFO @ Sat, 03 Apr 2021 06:55:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2333003/SRX2333003.20_model.r WARNING @ Sat, 03 Apr 2021 06:55:49: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:55:49: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Sat, 03 Apr 2021 06:55:49: #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 06:55:49: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:55:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:56:02: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:56:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2333003/SRX2333003.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:56:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2333003/SRX2333003.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:56:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2333003/SRX2333003.20_summits.bed INFO @ Sat, 03 Apr 2021 06:56:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (407 records, 4 fields): 2 millis CompletedMACS2peakCalling