[2024-01-25 18:48:50,763] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:48:50,765] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:48:50,765] [INFO] DQC Reference Directory: /var/lib/cwl/stg71fd689d-c5ab-4643-bb79-9e613fff0c87/dqc_reference
[2024-01-25 18:48:51,866] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:48:51,866] [INFO] Task started: Prodigal
[2024-01-25 18:48:51,867] [INFO] Running command: gunzip -c /var/lib/cwl/stg22ea610c-ae48-4f80-9a27-4ab88b19065c/GCF_030409505.1_ASM3040950v1_genomic.fna.gz | prodigal -d GCF_030409505.1_ASM3040950v1_genomic.fna/cds.fna -a GCF_030409505.1_ASM3040950v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:49:03,358] [INFO] Task succeeded: Prodigal
[2024-01-25 18:49:03,358] [INFO] Task started: HMMsearch
[2024-01-25 18:49:03,359] [INFO] Running command: hmmsearch --tblout GCF_030409505.1_ASM3040950v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71fd689d-c5ab-4643-bb79-9e613fff0c87/dqc_reference/reference_markers.hmm GCF_030409505.1_ASM3040950v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:49:03,641] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:49:03,642] [INFO] Found 6/6 markers.
[2024-01-25 18:49:03,679] [INFO] Query marker FASTA was written to GCF_030409505.1_ASM3040950v1_genomic.fna/markers.fasta
[2024-01-25 18:49:03,680] [INFO] Task started: Blastn
[2024-01-25 18:49:03,680] [INFO] Running command: blastn -query GCF_030409505.1_ASM3040950v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71fd689d-c5ab-4643-bb79-9e613fff0c87/dqc_reference/reference_markers.fasta -out GCF_030409505.1_ASM3040950v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:49:04,318] [INFO] Task succeeded: Blastn
[2024-01-25 18:49:04,321] [INFO] Selected 20 target genomes.
[2024-01-25 18:49:04,321] [INFO] Target genome list was writen to GCF_030409505.1_ASM3040950v1_genomic.fna/target_genomes.txt
[2024-01-25 18:49:04,339] [INFO] Task started: fastANI
[2024-01-25 18:49:04,339] [INFO] Running command: fastANI --query /var/lib/cwl/stg22ea610c-ae48-4f80-9a27-4ab88b19065c/GCF_030409505.1_ASM3040950v1_genomic.fna.gz --refList GCF_030409505.1_ASM3040950v1_genomic.fna/target_genomes.txt --output GCF_030409505.1_ASM3040950v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:49:18,062] [INFO] Task succeeded: fastANI
[2024-01-25 18:49:18,062] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71fd689d-c5ab-4643-bb79-9e613fff0c87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:49:18,062] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71fd689d-c5ab-4643-bb79-9e613fff0c87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:49:18,073] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:49:18,074] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:49:18,074] [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
Zunongwangia atlantica	strain=22II14-10F7	GCA_002094855.1	1502297	1502297	type	True	81.8471	868	1460	95	below_threshold
Zunongwangia mangrovi	strain=DSM 24499	GCA_900112105.1	1334022	1334022	type	True	81.7001	882	1460	95	below_threshold
Zunongwangia profunda	strain=SMA-87	GCA_000023465.1	398743	398743	type	True	81.0114	858	1460	95	below_threshold
Salegentibacter salegens	strain=ACAM 48	GCA_900142975.1	143223	143223	type	True	77.8325	300	1460	95	below_threshold
Salegentibacter mishustinae	strain=DSM 23404	GCA_002900095.1	270918	270918	type	True	77.6763	300	1460	95	below_threshold
Salegentibacter agarivorans	strain=DSM 23515	GCA_900113135.1	345907	345907	type	True	77.5942	308	1460	95	below_threshold
Salegentibacter salegens	strain=DSM 5424	GCA_003001895.1	143223	143223	type	True	77.5728	288	1460	95	below_threshold
Salegentibacter holothuriorum	strain=DSM 23405	GCA_900168045.1	241145	241145	type	True	77.5715	258	1460	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	77.5208	264	1460	95	below_threshold
Salegentibacter mishustinae	strain=KCTC 12263	GCA_001431365.1	270918	270918	type	True	77.4973	291	1460	95	below_threshold
Gramella crocea	strain=YB25	GCA_022410465.1	2904124	2904124	type	True	77.4156	121	1460	95	below_threshold
Salegentibacter mishustinae	strain=KCTC 12263	GCA_014651335.1	270918	270918	type	True	77.4032	289	1460	95	below_threshold
Salegentibacter maritimus	strain=F63223	GCA_016236915.1	2794347	2794347	type	True	77.2451	237	1460	95	below_threshold
Haloflavibacter putidus	strain=PLHSN227	GCA_006546625.1	2576776	2576776	type	True	77.1339	111	1460	95	below_threshold
Flavobacterium alkalisoli	strain=XS-5	GCA_008000935.1	2602769	2602769	type	True	77.0568	65	1460	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	76.9938	94	1460	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.8852	107	1460	95	below_threshold
Bizionia argentinensis	strain=JUB59	GCA_000224335.2	456455	456455	type	True	76.5139	78	1460	95	below_threshold
Aquimarina aggregata	strain=RZW4-3-2	GCA_001632745.1	1642818	1642818	type	True	76.2451	119	1460	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:49:18,075] [INFO] DFAST Taxonomy check result was written to GCF_030409505.1_ASM3040950v1_genomic.fna/tc_result.tsv
[2024-01-25 18:49:18,076] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:49:18,076] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:49:18,076] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71fd689d-c5ab-4643-bb79-9e613fff0c87/dqc_reference/checkm_data
[2024-01-25 18:49:18,077] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:49:18,117] [INFO] Task started: CheckM
[2024-01-25 18:49:18,117] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030409505.1_ASM3040950v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030409505.1_ASM3040950v1_genomic.fna/checkm_input GCF_030409505.1_ASM3040950v1_genomic.fna/checkm_result
[2024-01-25 18:49:53,776] [INFO] Task succeeded: CheckM
[2024-01-25 18:49:53,777] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:49:53,795] [INFO] ===== Completeness check finished =====
[2024-01-25 18:49:53,795] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:49:53,796] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030409505.1_ASM3040950v1_genomic.fna/markers.fasta)
[2024-01-25 18:49:53,796] [INFO] Task started: Blastn
[2024-01-25 18:49:53,796] [INFO] Running command: blastn -query GCF_030409505.1_ASM3040950v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71fd689d-c5ab-4643-bb79-9e613fff0c87/dqc_reference/reference_markers_gtdb.fasta -out GCF_030409505.1_ASM3040950v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:49:54,712] [INFO] Task succeeded: Blastn
[2024-01-25 18:49:54,714] [INFO] Selected 16 target genomes.
[2024-01-25 18:49:54,715] [INFO] Target genome list was writen to GCF_030409505.1_ASM3040950v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:49:54,733] [INFO] Task started: fastANI
[2024-01-25 18:49:54,733] [INFO] Running command: fastANI --query /var/lib/cwl/stg22ea610c-ae48-4f80-9a27-4ab88b19065c/GCF_030409505.1_ASM3040950v1_genomic.fna.gz --refList GCF_030409505.1_ASM3040950v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030409505.1_ASM3040950v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:50:05,849] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:05,859] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:50:05,859] [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_002094855.1	s__Zunongwangia atlantica	81.8467	867	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zunongwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112105.1	s__Zunongwangia mangrovi	81.7137	880	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zunongwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023465.1	s__Zunongwangia profunda	80.9737	858	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zunongwangia	95.0	99.17	98.44	0.93	0.80	11	-
GCF_000745315.1	s__Salegentibacter sp000745315	78.0858	283	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104765.1	s__Gillisia sp900104765	77.8375	197	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	98.23	98.23	0.92	0.92	2	-
GCF_900142975.1	s__Salegentibacter salegens	77.8368	300	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002900095.1	s__Salegentibacter mishustinae	77.6463	302	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	4	-
GCF_900113135.1	s__Salegentibacter agarivorans	77.6084	305	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	97.64	95.65	0.87	0.86	4	-
GCF_900168265.1	s__Salegentibacter salarius	77.5605	266	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	100.00	99.99	1.00	0.99	3	-
GCF_900168045.1	s__Salegentibacter holothuriorum	77.5542	258	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054225.1	s__Gramella gaetbulicola	77.4271	181	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009735585.1	s__Gramella aestuarii	77.2409	139	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016236915.1	s__Salegentibacter maritimus	77.1683	235	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	98.25	98.21	0.91	0.91	3	-
GCF_000224335.1	s__Algorimicrobium argentinense	76.5402	77	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111025.1	s__Jejuia jejuensis	76.5241	66	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016649785.1	s__Gillisia sp016649785	76.1211	76	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:50:05,860] [INFO] GTDB search result was written to GCF_030409505.1_ASM3040950v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:50:05,861] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:50:05,864] [INFO] DFAST_QC result json was written to GCF_030409505.1_ASM3040950v1_genomic.fna/dqc_result.json
[2024-01-25 18:50:05,864] [INFO] DFAST_QC completed!
[2024-01-25 18:50:05,865] [INFO] Total running time: 0h1m15s