[2024-01-24 12:29:26,867] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:26,869] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:26,869] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2511dfd-a871-4de0-936c-0dddb7f68730/dqc_reference
[2024-01-24 12:29:28,140] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:28,143] [INFO] Task started: Prodigal
[2024-01-24 12:29:28,143] [INFO] Running command: gunzip -c /var/lib/cwl/stgdab23c21-6ef7-41f3-add5-4c496354a46f/GCF_020164495.1_ASM2016449v1_genomic.fna.gz | prodigal -d GCF_020164495.1_ASM2016449v1_genomic.fna/cds.fna -a GCF_020164495.1_ASM2016449v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:39,733] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:39,734] [INFO] Task started: HMMsearch
[2024-01-24 12:29:39,734] [INFO] Running command: hmmsearch --tblout GCF_020164495.1_ASM2016449v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2511dfd-a871-4de0-936c-0dddb7f68730/dqc_reference/reference_markers.hmm GCF_020164495.1_ASM2016449v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:40,032] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:40,033] [INFO] Found 6/6 markers.
[2024-01-24 12:29:40,061] [INFO] Query marker FASTA was written to GCF_020164495.1_ASM2016449v1_genomic.fna/markers.fasta
[2024-01-24 12:29:40,061] [INFO] Task started: Blastn
[2024-01-24 12:29:40,061] [INFO] Running command: blastn -query GCF_020164495.1_ASM2016449v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2511dfd-a871-4de0-936c-0dddb7f68730/dqc_reference/reference_markers.fasta -out GCF_020164495.1_ASM2016449v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:40,732] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:40,735] [INFO] Selected 18 target genomes.
[2024-01-24 12:29:40,736] [INFO] Target genome list was writen to GCF_020164495.1_ASM2016449v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:40,745] [INFO] Task started: fastANI
[2024-01-24 12:29:40,745] [INFO] Running command: fastANI --query /var/lib/cwl/stgdab23c21-6ef7-41f3-add5-4c496354a46f/GCF_020164495.1_ASM2016449v1_genomic.fna.gz --refList GCF_020164495.1_ASM2016449v1_genomic.fna/target_genomes.txt --output GCF_020164495.1_ASM2016449v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:52,699] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:52,700] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2511dfd-a871-4de0-936c-0dddb7f68730/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:52,700] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2511dfd-a871-4de0-936c-0dddb7f68730/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:52,711] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:29:52,711] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:29:52,712] [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
Psychroflexus lacisalsi	strain=KACC 14089	GCA_020164495.1	503928	503928	type	True	100.0	1000	1000	95	conclusive
Psychroflexus gondwanensis	strain=ACAM 44	GCA_000355905.1	251	251	type	True	81.3598	415	1000	95	below_threshold
Psychroflexus torquis	strain=ATCC 700755	GCA_000153485.2	57029	57029	type	True	79.6655	361	1000	95	below_threshold
Psychroflexus sediminis	strain=DSM 19803	GCA_900099815.1	470826	470826	type	True	79.0322	449	1000	95	below_threshold
Psychroflexus aurantiacus	strain=YR1-1	GCA_010820555.1	2709310	2709310	type	True	78.8401	405	1000	95	below_threshold
Psychroflexus tropicus	strain=DSM 15496	GCA_000378765.1	197345	197345	type	True	78.2803	376	1000	95	below_threshold
Psychroflexus maritimus	strain=C1	GCA_011089875.1	2714865	2714865	type	True	76.7943	66	1000	95	below_threshold
Zunongwangia atlantica	strain=22II14-10F7	GCA_002094855.1	1502297	1502297	type	True	76.3216	74	1000	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	76.2722	60	1000	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	76.2265	52	1000	95	below_threshold
Zunongwangia mangrovi	strain=DSM 24499	GCA_900112105.1	1334022	1334022	type	True	76.1939	70	1000	95	below_threshold
Mesonia phycicola	strain=DSM 21425	GCA_900141885.1	579105	579105	type	True	76.0884	78	1000	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:52,714] [INFO] DFAST Taxonomy check result was written to GCF_020164495.1_ASM2016449v1_genomic.fna/tc_result.tsv
[2024-01-24 12:29:52,715] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:52,715] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:52,716] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2511dfd-a871-4de0-936c-0dddb7f68730/dqc_reference/checkm_data
[2024-01-24 12:29:52,718] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:52,751] [INFO] Task started: CheckM
[2024-01-24 12:29:52,751] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020164495.1_ASM2016449v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020164495.1_ASM2016449v1_genomic.fna/checkm_input GCF_020164495.1_ASM2016449v1_genomic.fna/checkm_result
[2024-01-24 12:30:31,844] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:31,845] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:31,884] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:31,884] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:31,885] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020164495.1_ASM2016449v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:31,886] [INFO] Task started: Blastn
[2024-01-24 12:30:31,886] [INFO] Running command: blastn -query GCF_020164495.1_ASM2016449v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2511dfd-a871-4de0-936c-0dddb7f68730/dqc_reference/reference_markers_gtdb.fasta -out GCF_020164495.1_ASM2016449v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:32,812] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:32,815] [INFO] Selected 21 target genomes.
[2024-01-24 12:30:32,815] [INFO] Target genome list was writen to GCF_020164495.1_ASM2016449v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:32,835] [INFO] Task started: fastANI
[2024-01-24 12:30:32,835] [INFO] Running command: fastANI --query /var/lib/cwl/stgdab23c21-6ef7-41f3-add5-4c496354a46f/GCF_020164495.1_ASM2016449v1_genomic.fna.gz --refList GCF_020164495.1_ASM2016449v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020164495.1_ASM2016449v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:44,914] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:44,930] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:30:44,931] [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_000355905.1	s__Psychroflexus gondwanensis	81.3703	414	1000	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	98.53	98.53	0.91	0.91	2	-
GCF_000153485.2	s__Psychroflexus torquis	79.6655	361	1000	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836055.1	s__Psychroflexus sp002836055	79.1051	326	1000	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099815.1	s__Psychroflexus sediminis	79.0322	449	1000	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010820555.1	s__Psychroflexus sp010820555	78.8401	405	1000	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378765.1	s__Psychroflexus tropicus	78.2803	376	1000	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003565575.1	s__Psychroflexus sp003565575	77.826	229	1000	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004010055.1	s__Psychroflexus aestuariivivens	77.4708	220	1000	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011089875.1	s__Psychroflexus maritimus	76.7943	66	1000	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009741275.1	s__Winogradskyella endarachnes	76.6433	55	1000	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640195.1	s__Psychroflexus planctonicus	76.3912	104	1000	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002094855.1	s__Zunongwangia atlantica	76.3216	74	1000	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zunongwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667275.1	s__Mesonia aquimarina	76.2128	65	1000	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112105.1	s__Zunongwangia mangrovi	76.1939	70	1000	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zunongwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141885.1	s__Mesonia phycicola	76.0884	78	1000	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860825.1	s__Oceanihabitans sp018860825	75.985	56	1000	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:30:44,932] [INFO] GTDB search result was written to GCF_020164495.1_ASM2016449v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:44,933] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:44,937] [INFO] DFAST_QC result json was written to GCF_020164495.1_ASM2016449v1_genomic.fna/dqc_result.json
[2024-01-24 12:30:44,937] [INFO] DFAST_QC completed!
[2024-01-24 12:30:44,937] [INFO] Total running time: 0h1m18s