[2024-01-25 17:43:20,643] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:43:20,645] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:43:20,645] [INFO] DQC Reference Directory: /var/lib/cwl/stg75bb9a98-e5b4-4c8c-9b00-d576907c3841/dqc_reference
[2024-01-25 17:43:21,791] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:43:21,791] [INFO] Task started: Prodigal
[2024-01-25 17:43:21,791] [INFO] Running command: gunzip -c /var/lib/cwl/stg989ef741-4350-47df-a543-be308adf7c0c/GCF_003254355.1_ASM325435v1_genomic.fna.gz | prodigal -d GCF_003254355.1_ASM325435v1_genomic.fna/cds.fna -a GCF_003254355.1_ASM325435v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:43:38,744] [INFO] Task succeeded: Prodigal
[2024-01-25 17:43:38,745] [INFO] Task started: HMMsearch
[2024-01-25 17:43:38,745] [INFO] Running command: hmmsearch --tblout GCF_003254355.1_ASM325435v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg75bb9a98-e5b4-4c8c-9b00-d576907c3841/dqc_reference/reference_markers.hmm GCF_003254355.1_ASM325435v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:43:38,987] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:43:38,988] [INFO] Found 6/6 markers.
[2024-01-25 17:43:39,025] [INFO] Query marker FASTA was written to GCF_003254355.1_ASM325435v1_genomic.fna/markers.fasta
[2024-01-25 17:43:39,025] [INFO] Task started: Blastn
[2024-01-25 17:43:39,025] [INFO] Running command: blastn -query GCF_003254355.1_ASM325435v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75bb9a98-e5b4-4c8c-9b00-d576907c3841/dqc_reference/reference_markers.fasta -out GCF_003254355.1_ASM325435v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:39,577] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:39,580] [INFO] Selected 9 target genomes.
[2024-01-25 17:43:39,580] [INFO] Target genome list was writen to GCF_003254355.1_ASM325435v1_genomic.fna/target_genomes.txt
[2024-01-25 17:43:39,588] [INFO] Task started: fastANI
[2024-01-25 17:43:39,588] [INFO] Running command: fastANI --query /var/lib/cwl/stg989ef741-4350-47df-a543-be308adf7c0c/GCF_003254355.1_ASM325435v1_genomic.fna.gz --refList GCF_003254355.1_ASM325435v1_genomic.fna/target_genomes.txt --output GCF_003254355.1_ASM325435v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:43:50,052] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:50,052] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg75bb9a98-e5b4-4c8c-9b00-d576907c3841/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:43:50,053] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg75bb9a98-e5b4-4c8c-9b00-d576907c3841/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:43:50,059] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:43:50,060] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:43:50,060] [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
Algoriphagus ratkowskyi	strain=DSM 22686	GCA_003254355.1	57028	57028	type	True	100.0	1637	1640	95	conclusive
Algoriphagus ratkowskyi	strain=DSM 22686	GCA_002150505.1	57028	57028	type	True	99.9799	1614	1640	95	conclusive
Algoriphagus aquimarinus	strain=DSM 23399	GCA_900112005.1	237018	237018	type	True	83.0487	951	1640	95	below_threshold
Algoriphagus antarcticus	strain=DSM 15986	GCA_003387655.1	238540	238540	type	True	80.6908	954	1640	95	below_threshold
Algoriphagus chordae	strain=DSM 19830	GCA_003254055.1	237019	237019	type	True	80.6893	835	1640	95	below_threshold
Algoriphagus antarcticus	strain=DSM 15986	GCA_002150685.1	238540	238540	type	True	80.6666	955	1640	95	below_threshold
Algoriphagus locisalis	strain=DSM 23445	GCA_900116615.1	305507	305507	type	True	80.0692	707	1640	95	below_threshold
Algoriphagus yeomjeoni	strain=DSM 23446	GCA_003259505.1	291403	291403	type	True	79.7803	760	1640	95	below_threshold
Belliella aquatica	strain=JCM 19468	GCA_022549755.1	1323734	1323734	type	True	76.8755	99	1640	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:43:50,061] [INFO] DFAST Taxonomy check result was written to GCF_003254355.1_ASM325435v1_genomic.fna/tc_result.tsv
[2024-01-25 17:43:50,062] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:43:50,062] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:43:50,062] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg75bb9a98-e5b4-4c8c-9b00-d576907c3841/dqc_reference/checkm_data
[2024-01-25 17:43:50,063] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:43:50,116] [INFO] Task started: CheckM
[2024-01-25 17:43:50,116] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003254355.1_ASM325435v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003254355.1_ASM325435v1_genomic.fna/checkm_input GCF_003254355.1_ASM325435v1_genomic.fna/checkm_result
[2024-01-25 17:44:40,502] [INFO] Task succeeded: CheckM
[2024-01-25 17:44:40,503] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:44:40,523] [INFO] ===== Completeness check finished =====
[2024-01-25 17:44:40,523] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:44:40,524] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003254355.1_ASM325435v1_genomic.fna/markers.fasta)
[2024-01-25 17:44:40,524] [INFO] Task started: Blastn
[2024-01-25 17:44:40,525] [INFO] Running command: blastn -query GCF_003254355.1_ASM325435v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75bb9a98-e5b4-4c8c-9b00-d576907c3841/dqc_reference/reference_markers_gtdb.fasta -out GCF_003254355.1_ASM325435v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:41,357] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:41,361] [INFO] Selected 9 target genomes.
[2024-01-25 17:44:41,362] [INFO] Target genome list was writen to GCF_003254355.1_ASM325435v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:44:41,369] [INFO] Task started: fastANI
[2024-01-25 17:44:41,369] [INFO] Running command: fastANI --query /var/lib/cwl/stg989ef741-4350-47df-a543-be308adf7c0c/GCF_003254355.1_ASM325435v1_genomic.fna.gz --refList GCF_003254355.1_ASM325435v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003254355.1_ASM325435v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:44:50,731] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:50,738] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:44:50,738] [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_002150505.1	s__Algoriphagus ratkowskyi	99.9799	1614	1640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	99.99	1.00	1.00	3	conclusive
GCF_900112005.1	s__Algoriphagus aquimarinus	83.043	952	1640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997215.1	s__Algoriphagus aquimarinus_A	81.5934	888	1640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254055.1	s__Algoriphagus chordae	80.6919	835	1640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002150685.1	s__Algoriphagus antarcticus	80.6649	955	1640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900116615.1	s__Algoriphagus locisalis	80.0692	707	1640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259505.1	s__Algoriphagus yeomjeoni	79.7832	760	1640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014324365.1	s__Algoriphagus sp014324365	77.1412	155	1640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:44:50,741] [INFO] GTDB search result was written to GCF_003254355.1_ASM325435v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:44:50,741] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:44:50,744] [INFO] DFAST_QC result json was written to GCF_003254355.1_ASM325435v1_genomic.fna/dqc_result.json
[2024-01-25 17:44:50,744] [INFO] DFAST_QC completed!
[2024-01-25 17:44:50,744] [INFO] Total running time: 0h1m30s