[2024-01-24 12:40:04,070] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:04,071] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:04,072] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e94be65-54ed-4f77-a2a7-509b746fcfa8/dqc_reference
[2024-01-24 12:40:05,300] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:05,301] [INFO] Task started: Prodigal
[2024-01-24 12:40:05,301] [INFO] Running command: gunzip -c /var/lib/cwl/stg667c1226-56fc-4358-836b-3b69fd5cc802/GCF_019957155.1_ASM1995715v1_genomic.fna.gz | prodigal -d GCF_019957155.1_ASM1995715v1_genomic.fna/cds.fna -a GCF_019957155.1_ASM1995715v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:09,589] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:09,589] [INFO] Task started: HMMsearch
[2024-01-24 12:40:09,589] [INFO] Running command: hmmsearch --tblout GCF_019957155.1_ASM1995715v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e94be65-54ed-4f77-a2a7-509b746fcfa8/dqc_reference/reference_markers.hmm GCF_019957155.1_ASM1995715v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:09,820] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:09,821] [INFO] Found 6/6 markers.
[2024-01-24 12:40:09,855] [INFO] Query marker FASTA was written to GCF_019957155.1_ASM1995715v1_genomic.fna/markers.fasta
[2024-01-24 12:40:09,856] [INFO] Task started: Blastn
[2024-01-24 12:40:09,856] [INFO] Running command: blastn -query GCF_019957155.1_ASM1995715v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e94be65-54ed-4f77-a2a7-509b746fcfa8/dqc_reference/reference_markers.fasta -out GCF_019957155.1_ASM1995715v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:10,433] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:10,437] [INFO] Selected 7 target genomes.
[2024-01-24 12:40:10,437] [INFO] Target genome list was writen to GCF_019957155.1_ASM1995715v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:10,446] [INFO] Task started: fastANI
[2024-01-24 12:40:10,446] [INFO] Running command: fastANI --query /var/lib/cwl/stg667c1226-56fc-4358-836b-3b69fd5cc802/GCF_019957155.1_ASM1995715v1_genomic.fna.gz --refList GCF_019957155.1_ASM1995715v1_genomic.fna/target_genomes.txt --output GCF_019957155.1_ASM1995715v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:14,282] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:14,283] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e94be65-54ed-4f77-a2a7-509b746fcfa8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:14,284] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e94be65-54ed-4f77-a2a7-509b746fcfa8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:14,295] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:40:14,295] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:14,296] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Anaerococcus murdochii	strain=FDAARGOS_1460	GCA_019957155.1	411577	411577	type	True	100.0	746	749	95	conclusive
Anaerococcus degeneri	strain=FDAARGOS_1538	GCA_020215685.1	361500	361500	type	True	91.4364	570	749	95	below_threshold
Anaerococcus degeneri	strain=DSM 29674	GCA_017874475.1	361500	361500	type	True	91.3767	560	749	95	below_threshold
Anaerococcus lactolyticus	strain=ATCC 51172	GCA_000156575.1	33032	33032	type	True	85.3352	492	749	95	below_threshold
Anaerococcus mediterraneensis	strain=Marseille-P2765	GCA_900128415.1	1870984	1870984	type	True	83.0552	342	749	95	below_threshold
Anaerococcus urinomassiliensis	strain=Marseille-P2143	GCA_900128425.1	1745712	1745712	type	True	81.6375	154	749	95	below_threshold
Anaerococcus tetradius	strain=ATCC 35098	GCA_000159095.1	33036	33036	type	True	80.5065	177	749	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:14,297] [INFO] DFAST Taxonomy check result was written to GCF_019957155.1_ASM1995715v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:14,297] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:14,298] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:14,298] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e94be65-54ed-4f77-a2a7-509b746fcfa8/dqc_reference/checkm_data
[2024-01-24 12:40:14,299] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:14,323] [INFO] Task started: CheckM
[2024-01-24 12:40:14,323] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019957155.1_ASM1995715v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019957155.1_ASM1995715v1_genomic.fna/checkm_input GCF_019957155.1_ASM1995715v1_genomic.fna/checkm_result
[2024-01-24 12:40:34,467] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:34,468] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:34,491] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:34,492] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:34,492] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019957155.1_ASM1995715v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:34,492] [INFO] Task started: Blastn
[2024-01-24 12:40:34,493] [INFO] Running command: blastn -query GCF_019957155.1_ASM1995715v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e94be65-54ed-4f77-a2a7-509b746fcfa8/dqc_reference/reference_markers_gtdb.fasta -out GCF_019957155.1_ASM1995715v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:35,317] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:35,322] [INFO] Selected 9 target genomes.
[2024-01-24 12:40:35,323] [INFO] Target genome list was writen to GCF_019957155.1_ASM1995715v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:35,342] [INFO] Task started: fastANI
[2024-01-24 12:40:35,342] [INFO] Running command: fastANI --query /var/lib/cwl/stg667c1226-56fc-4358-836b-3b69fd5cc802/GCF_019957155.1_ASM1995715v1_genomic.fna.gz --refList GCF_019957155.1_ASM1995715v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019957155.1_ASM1995715v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:39,424] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:39,437] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:40:39,437] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_017874475.1	s__Anaerococcus degeneri	91.3767	560	749	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000156575.1	s__Anaerococcus lactolyticus	85.2867	496	749	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	97.67	97.67	0.89	0.89	2	-
GCF_900128415.1	s__Anaerococcus mediterraneensis	83.0743	340	749	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551095.1	s__Anaerococcus sp900551095	82.5215	247	749	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900258475.1	s__Anaerococcus sp900258475	81.7787	369	749	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	96.55	96.55	0.87	0.87	2	-
GCA_000308255.3	s__Anaerococcus pacaensis	81.1252	128	749	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	99.91	99.91	0.98	0.98	2	-
GCA_900550345.1	s__Anaerococcus sp900550345	81.014	82	749	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900290195.1	s__Anaerococcus marasmi	80.7704	163	749	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000159095.1	s__Anaerococcus tetradius	80.4763	179	749	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	98.20	98.20	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:40:39,439] [INFO] GTDB search result was written to GCF_019957155.1_ASM1995715v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:39,440] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:39,442] [INFO] DFAST_QC result json was written to GCF_019957155.1_ASM1995715v1_genomic.fna/dqc_result.json
[2024-01-24 12:40:39,442] [INFO] DFAST_QC completed!
[2024-01-24 12:40:39,443] [INFO] Total running time: 0h0m35s