[2023-06-28 12:01:25,565] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:01:25,567] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:01:25,567] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c694fa1-d6ea-4d89-a28d-101df3db7d9c/dqc_reference
[2023-06-28 12:01:26,820] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:01:26,821] [INFO] Task started: Prodigal
[2023-06-28 12:01:26,822] [INFO] Running command: gunzip -c /var/lib/cwl/stgf71be882-5f6d-43b2-a292-d43cd178bca4/GCA_020436485.1_ASM2043648v1_genomic.fna.gz | prodigal -d GCA_020436485.1_ASM2043648v1_genomic.fna/cds.fna -a GCA_020436485.1_ASM2043648v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:02:01,403] [INFO] Task succeeded: Prodigal
[2023-06-28 12:02:01,404] [INFO] Task started: HMMsearch
[2023-06-28 12:02:01,404] [INFO] Running command: hmmsearch --tblout GCA_020436485.1_ASM2043648v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c694fa1-d6ea-4d89-a28d-101df3db7d9c/dqc_reference/reference_markers.hmm GCA_020436485.1_ASM2043648v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:02:01,739] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:02:01,741] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgf71be882-5f6d-43b2-a292-d43cd178bca4/GCA_020436485.1_ASM2043648v1_genomic.fna.gz]
[2023-06-28 12:02:01,810] [INFO] Query marker FASTA was written to GCA_020436485.1_ASM2043648v1_genomic.fna/markers.fasta
[2023-06-28 12:02:01,810] [INFO] Task started: Blastn
[2023-06-28 12:02:01,810] [INFO] Running command: blastn -query GCA_020436485.1_ASM2043648v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c694fa1-d6ea-4d89-a28d-101df3db7d9c/dqc_reference/reference_markers.fasta -out GCA_020436485.1_ASM2043648v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:02:02,530] [INFO] Task succeeded: Blastn
[2023-06-28 12:02:02,536] [INFO] Selected 18 target genomes.
[2023-06-28 12:02:02,537] [INFO] Target genome list was writen to GCA_020436485.1_ASM2043648v1_genomic.fna/target_genomes.txt
[2023-06-28 12:02:02,546] [INFO] Task started: fastANI
[2023-06-28 12:02:02,546] [INFO] Running command: fastANI --query /var/lib/cwl/stgf71be882-5f6d-43b2-a292-d43cd178bca4/GCA_020436485.1_ASM2043648v1_genomic.fna.gz --refList GCA_020436485.1_ASM2043648v1_genomic.fna/target_genomes.txt --output GCA_020436485.1_ASM2043648v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:02:18,395] [INFO] Task succeeded: fastANI
[2023-06-28 12:02:18,396] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c694fa1-d6ea-4d89-a28d-101df3db7d9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:02:18,397] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c694fa1-d6ea-4d89-a28d-101df3db7d9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:02:18,409] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:02:18,409] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 12:02:18,409] [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
Neolewinella maritima	strain=CECT 8419, type strain	GCA_923081025.1	1383882	1383882	type	True	75.8637	60	1612	95	below_threshold
Neolewinella marina	strain=MKG-38	GCA_002631205.1	438751	438751	type	True	75.846	99	1612	95	below_threshold
Neolewinella marina	strain=DSM 104084	GCA_011927705.1	438751	438751	type	True	75.8446	97	1612	95	below_threshold
Neolewinella litorea	strain=HSMS-39	GCA_004803465.1	2562452	2562452	type	True	75.558	68	1612	95	below_threshold
Hymenobacter terricola	strain=3F2	GCA_017921975.2	2819236	2819236	type	True	75.1777	59	1612	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	75.0457	53	1612	95	below_threshold
Hymenobacter chitinivorans	strain=DSM 11115	GCA_002797555.1	89969	89969	type	True	75.0343	59	1612	95	below_threshold
Hymenobacter aquaticus	strain=JCM 31653	GCA_004765605.1	1867101	1867101	type	True	75.0043	56	1612	95	below_threshold
Azospirillum palustre	strain=B2	GCA_002573965.1	2044885	2044885	type	True	74.7993	52	1612	95	below_threshold
Nitrospirillum iridis	strain=DSM 22198	GCA_014205765.1	765888	765888	type	True	74.7454	52	1612	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 12:02:18,412] [INFO] DFAST Taxonomy check result was written to GCA_020436485.1_ASM2043648v1_genomic.fna/tc_result.tsv
[2023-06-28 12:02:18,413] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:02:18,413] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:02:18,414] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c694fa1-d6ea-4d89-a28d-101df3db7d9c/dqc_reference/checkm_data
[2023-06-28 12:02:18,415] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:02:18,502] [INFO] Task started: CheckM
[2023-06-28 12:02:18,503] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020436485.1_ASM2043648v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020436485.1_ASM2043648v1_genomic.fna/checkm_input GCA_020436485.1_ASM2043648v1_genomic.fna/checkm_result
[2023-06-28 12:03:46,643] [INFO] Task succeeded: CheckM
[2023-06-28 12:03:46,645] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.61%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:03:46,672] [INFO] ===== Completeness check finished =====
[2023-06-28 12:03:46,673] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:03:46,674] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020436485.1_ASM2043648v1_genomic.fna/markers.fasta)
[2023-06-28 12:03:46,675] [INFO] Task started: Blastn
[2023-06-28 12:03:46,675] [INFO] Running command: blastn -query GCA_020436485.1_ASM2043648v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c694fa1-d6ea-4d89-a28d-101df3db7d9c/dqc_reference/reference_markers_gtdb.fasta -out GCA_020436485.1_ASM2043648v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:03:47,873] [INFO] Task succeeded: Blastn
[2023-06-28 12:03:47,877] [INFO] Selected 27 target genomes.
[2023-06-28 12:03:47,877] [INFO] Target genome list was writen to GCA_020436485.1_ASM2043648v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:03:47,915] [INFO] Task started: fastANI
[2023-06-28 12:03:47,915] [INFO] Running command: fastANI --query /var/lib/cwl/stgf71be882-5f6d-43b2-a292-d43cd178bca4/GCA_020436485.1_ASM2043648v1_genomic.fna.gz --refList GCA_020436485.1_ASM2043648v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020436485.1_ASM2043648v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:04:11,331] [INFO] Task succeeded: fastANI
[2023-06-28 12:04:11,344] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 12:04:11,344] [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
GCA_016703765.1	s__JADJTT01 sp016703765	76.4357	88	1612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__JADJTT01	95.0	98.25	98.24	0.94	0.92	3	-
GCA_009908745.1	s__Phaeodactylibacter sp009908745	76.2031	119	1612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Phaeodactylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015490175.1	s__WFYJ01 sp015490175	76.0551	92	1612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__WFYJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014349155.1	s__Lewinella_A lacunae	75.9163	71	1612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002631205.1	s__Lewinella_A marina	75.846	99	1612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003045895.1	s__Lewinella sp003045895	75.833	77	1612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella	95.0	99.87	99.87	0.95	0.95	2	-
GCA_016715405.1	s__JABWBR01 sp016715405	75.7423	86	1612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__JABWBR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013360405.1	s__JABWBR01 sp013360405	75.7109	96	1612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__JABWBR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004803465.1	s__Lewinella_A litorea	75.558	68	1612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002646595.1	s__Flavilitoribacter nigricans	75.52	86	1612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Flavilitoribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787505.1	s__JABWBR01 sp016787505	75.3423	55	1612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__JABWBR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719895.1	s__M3007 sp016719895	75.2893	57	1612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	99.47	99.47	0.95	0.95	2	-
GCF_000333275.1	s__Nitrospirillum sp000333275	74.8115	58	1612	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:04:11,346] [INFO] GTDB search result was written to GCA_020436485.1_ASM2043648v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:04:11,347] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:04:11,350] [INFO] DFAST_QC result json was written to GCA_020436485.1_ASM2043648v1_genomic.fna/dqc_result.json
[2023-06-28 12:04:11,351] [INFO] DFAST_QC completed!
[2023-06-28 12:04:11,351] [INFO] Total running time: 0h2m46s