Job ID = 14160343 SRX = SRX9567170 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 27040874 spots for SRR13125145/SRR13125145.sra Written 27040874 spots for SRR13125145/SRR13125145.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160683 ("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: 01:38:38 27040874 reads; of these: 27040874 (100.00%) were paired; of these: 8122034 (30.04%) aligned concordantly 0 times 7958658 (29.43%) aligned concordantly exactly 1 time 10960182 (40.53%) aligned concordantly >1 times ---- 8122034 pairs aligned concordantly 0 times; of these: 4883260 (60.12%) aligned discordantly 1 time ---- 3238774 pairs aligned 0 times concordantly or discordantly; of these: 6477548 mates make up the pairs; of these: 3618900 (55.87%) aligned 0 times 1148394 (17.73%) aligned exactly 1 time 1710254 (26.40%) aligned >1 times 93.31% overall alignment rate Time searching: 01:38:38 Overall time: 01:38:38 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 40 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] 19019426 / 23757401 = 0.8006 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 @ Thu, 09 Dec 2021 03:27:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567170/SRX9567170.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567170/SRX9567170.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567170/SRX9567170.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567170/SRX9567170.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 @ Thu, 09 Dec 2021 03:27:10: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:27:10: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:27:18: 1000000 INFO @ Thu, 09 Dec 2021 03:27:25: 2000000 INFO @ Thu, 09 Dec 2021 03:27:32: 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 @ Thu, 09 Dec 2021 03:27:39: 4000000 INFO @ Thu, 09 Dec 2021 03:27:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567170/SRX9567170.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567170/SRX9567170.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567170/SRX9567170.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567170/SRX9567170.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 @ Thu, 09 Dec 2021 03:27:41: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:27:41: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:27:47: 5000000 INFO @ Thu, 09 Dec 2021 03:27:50: 1000000 INFO @ Thu, 09 Dec 2021 03:27:57: 6000000 INFO @ Thu, 09 Dec 2021 03:27:59: 2000000 INFO @ Thu, 09 Dec 2021 03:28:06: 7000000 INFO @ Thu, 09 Dec 2021 03:28:08: 3000000 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 @ Thu, 09 Dec 2021 03:28:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567170/SRX9567170.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567170/SRX9567170.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567170/SRX9567170.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567170/SRX9567170.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 @ Thu, 09 Dec 2021 03:28:11: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:28:11: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:28:15: 8000000 INFO @ Thu, 09 Dec 2021 03:28:18: 4000000 INFO @ Thu, 09 Dec 2021 03:28:20: 1000000 INFO @ Thu, 09 Dec 2021 03:28:24: 9000000 INFO @ Thu, 09 Dec 2021 03:28:27: 5000000 INFO @ Thu, 09 Dec 2021 03:28:30: 2000000 INFO @ Thu, 09 Dec 2021 03:28:33: 10000000 INFO @ Thu, 09 Dec 2021 03:28:36: 6000000 INFO @ Thu, 09 Dec 2021 03:28:39: 3000000 INFO @ Thu, 09 Dec 2021 03:28:43: 11000000 INFO @ Thu, 09 Dec 2021 03:28:45: 7000000 INFO @ Thu, 09 Dec 2021 03:28:48: 4000000 INFO @ Thu, 09 Dec 2021 03:28:52: 12000000 INFO @ Thu, 09 Dec 2021 03:28:54: 8000000 INFO @ Thu, 09 Dec 2021 03:28:55: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:28:55: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:28:55: #1 total tags in treatment: 3741739 INFO @ Thu, 09 Dec 2021 03:28:55: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:28:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:28:55: #1 tags after filtering in treatment: 2036113 INFO @ Thu, 09 Dec 2021 03:28:55: #1 Redundant rate of treatment: 0.46 INFO @ Thu, 09 Dec 2021 03:28:55: #1 finished! INFO @ Thu, 09 Dec 2021 03:28:55: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:28:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:28:56: #2 number of paired peaks: 1054 INFO @ Thu, 09 Dec 2021 03:28:56: start model_add_line... INFO @ Thu, 09 Dec 2021 03:28:56: start X-correlation... INFO @ Thu, 09 Dec 2021 03:28:56: end of X-cor INFO @ Thu, 09 Dec 2021 03:28:56: #2 finished! INFO @ Thu, 09 Dec 2021 03:28:56: #2 predicted fragment length is 298 bps INFO @ Thu, 09 Dec 2021 03:28:56: #2 alternative fragment length(s) may be 298 bps INFO @ Thu, 09 Dec 2021 03:28:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567170/SRX9567170.05_model.r WARNING @ Thu, 09 Dec 2021 03:28:56: #2 Since the d (298) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:28:56: #2 You may need to consider one of the other alternative d(s): 298 WARNING @ Thu, 09 Dec 2021 03:28:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:28:56: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:28:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:28:57: 5000000 INFO @ Thu, 09 Dec 2021 03:29:02: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:29:03: 9000000 INFO @ Thu, 09 Dec 2021 03:29:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567170/SRX9567170.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:29:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567170/SRX9567170.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:29:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567170/SRX9567170.05_summits.bed INFO @ Thu, 09 Dec 2021 03:29:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (764 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:29:06: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:29:12: 10000000 INFO @ Thu, 09 Dec 2021 03:29:15: 7000000 INFO @ Thu, 09 Dec 2021 03:29:21: 11000000 INFO @ Thu, 09 Dec 2021 03:29:24: 8000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:29:30: 12000000 INFO @ Thu, 09 Dec 2021 03:29:33: 9000000 INFO @ Thu, 09 Dec 2021 03:29:33: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:29:33: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:29:33: #1 total tags in treatment: 3741739 INFO @ Thu, 09 Dec 2021 03:29:33: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:29:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:29:33: #1 tags after filtering in treatment: 2036113 INFO @ Thu, 09 Dec 2021 03:29:33: #1 Redundant rate of treatment: 0.46 INFO @ Thu, 09 Dec 2021 03:29:33: #1 finished! INFO @ Thu, 09 Dec 2021 03:29:33: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:29:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:29:34: #2 number of paired peaks: 1054 INFO @ Thu, 09 Dec 2021 03:29:34: start model_add_line... INFO @ Thu, 09 Dec 2021 03:29:34: start X-correlation... INFO @ Thu, 09 Dec 2021 03:29:34: end of X-cor INFO @ Thu, 09 Dec 2021 03:29:34: #2 finished! INFO @ Thu, 09 Dec 2021 03:29:34: #2 predicted fragment length is 298 bps INFO @ Thu, 09 Dec 2021 03:29:34: #2 alternative fragment length(s) may be 298 bps INFO @ Thu, 09 Dec 2021 03:29:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567170/SRX9567170.10_model.r WARNING @ Thu, 09 Dec 2021 03:29:34: #2 Since the d (298) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:29:34: #2 You may need to consider one of the other alternative d(s): 298 WARNING @ Thu, 09 Dec 2021 03:29:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:29:34: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:29:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:29:40: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:29:40: 10000000 INFO @ Thu, 09 Dec 2021 03:29:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567170/SRX9567170.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:29:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567170/SRX9567170.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:29:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567170/SRX9567170.10_summits.bed INFO @ Thu, 09 Dec 2021 03:29:42: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (602 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:29:48: 11000000 INFO @ Thu, 09 Dec 2021 03:29:55: 12000000 INFO @ Thu, 09 Dec 2021 03:29:58: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:29:58: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:29:58: #1 total tags in treatment: 3741739 INFO @ Thu, 09 Dec 2021 03:29:58: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:29:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:29:58: #1 tags after filtering in treatment: 2036113 INFO @ Thu, 09 Dec 2021 03:29:58: #1 Redundant rate of treatment: 0.46 INFO @ Thu, 09 Dec 2021 03:29:58: #1 finished! INFO @ Thu, 09 Dec 2021 03:29:58: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:29:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:29:58: #2 number of paired peaks: 1054 INFO @ Thu, 09 Dec 2021 03:29:58: start model_add_line... INFO @ Thu, 09 Dec 2021 03:29:58: start X-correlation... INFO @ Thu, 09 Dec 2021 03:29:58: end of X-cor INFO @ Thu, 09 Dec 2021 03:29:58: #2 finished! INFO @ Thu, 09 Dec 2021 03:29:58: #2 predicted fragment length is 298 bps INFO @ Thu, 09 Dec 2021 03:29:58: #2 alternative fragment length(s) may be 298 bps INFO @ Thu, 09 Dec 2021 03:29:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567170/SRX9567170.20_model.r WARNING @ Thu, 09 Dec 2021 03:29:58: #2 Since the d (298) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:29:58: #2 You may need to consider one of the other alternative d(s): 298 WARNING @ Thu, 09 Dec 2021 03:29:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:29:58: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:29:58: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:30:05: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:30:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567170/SRX9567170.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:30:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567170/SRX9567170.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:30:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567170/SRX9567170.20_summits.bed INFO @ Thu, 09 Dec 2021 03:30:07: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (453 records, 4 fields): 2 millis CompletedMACS2peakCalling