[2024-01-24 11:05:23,877] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:23,880] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:23,881] [INFO] DQC Reference Directory: /var/lib/cwl/stg19d3502a-e304-4f22-bce4-04f9a2709f47/dqc_reference
[2024-01-24 11:05:25,538] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:25,540] [INFO] Task started: Prodigal
[2024-01-24 11:05:25,541] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d28d938-6b9c-41b8-a733-ee8150e0f3a7/GCF_002094855.1_ASM209485v1_genomic.fna.gz | prodigal -d GCF_002094855.1_ASM209485v1_genomic.fna/cds.fna -a GCF_002094855.1_ASM209485v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:40,441] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:40,441] [INFO] Task started: HMMsearch
[2024-01-24 11:05:40,441] [INFO] Running command: hmmsearch --tblout GCF_002094855.1_ASM209485v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19d3502a-e304-4f22-bce4-04f9a2709f47/dqc_reference/reference_markers.hmm GCF_002094855.1_ASM209485v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:40,766] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:40,768] [INFO] Found 6/6 markers.
[2024-01-24 11:05:40,814] [INFO] Query marker FASTA was written to GCF_002094855.1_ASM209485v1_genomic.fna/markers.fasta
[2024-01-24 11:05:40,814] [INFO] Task started: Blastn
[2024-01-24 11:05:40,814] [INFO] Running command: blastn -query GCF_002094855.1_ASM209485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19d3502a-e304-4f22-bce4-04f9a2709f47/dqc_reference/reference_markers.fasta -out GCF_002094855.1_ASM209485v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:41,519] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:41,522] [INFO] Selected 19 target genomes.
[2024-01-24 11:05:41,523] [INFO] Target genome list was writen to GCF_002094855.1_ASM209485v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:41,531] [INFO] Task started: fastANI
[2024-01-24 11:05:41,531] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d28d938-6b9c-41b8-a733-ee8150e0f3a7/GCF_002094855.1_ASM209485v1_genomic.fna.gz --refList GCF_002094855.1_ASM209485v1_genomic.fna/target_genomes.txt --output GCF_002094855.1_ASM209485v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:55,803] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:55,803] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19d3502a-e304-4f22-bce4-04f9a2709f47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:55,804] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19d3502a-e304-4f22-bce4-04f9a2709f47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:55,821] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:05:55,821] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:55,822] [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	100.0	1553	1555	95	conclusive
Zunongwangia mangrovi	strain=DSM 24499	GCA_900112105.1	1334022	1334022	type	True	91.5696	1157	1555	95	below_threshold
Zunongwangia profunda	strain=SMA-87	GCA_000023465.1	398743	398743	type	True	84.095	1087	1555	95	below_threshold
Mesonia mobilis	strain=DSM 19841	GCA_000423405.1	369791	369791	type	True	79.594	233	1555	95	below_threshold
Mesonia mobilis	strain=KCTC 12708	GCA_014651475.1	369791	369791	type	True	79.4984	242	1555	95	below_threshold
Salegentibacter agarivorans	strain=DSM 23515	GCA_900113135.1	345907	345907	type	True	78.3275	326	1555	95	below_threshold
Salegentibacter tibetensis	strain=JZCK2	GCA_020164485.1	2873600	2873600	type	True	77.7898	268	1555	95	below_threshold
Salegentibacter salegens	strain=DSM 5424	GCA_003001895.1	143223	143223	type	True	77.7489	291	1555	95	below_threshold
Salegentibacter salegens	strain=ACAM 48	GCA_900142975.1	143223	143223	type	True	77.7224	286	1555	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	77.6648	290	1555	95	below_threshold
Salegentibacter maritimus	strain=F63223	GCA_016236915.1	2794347	2794347	type	True	77.555	246	1555	95	below_threshold
Salegentibacter salarius	strain=KCTC 12974	GCA_002833385.1	435906	435906	type	True	77.5293	283	1555	95	below_threshold
Salegentibacter sediminis	strain=K5023	GCA_002078605.1	1930251	1930251	type	True	77.4676	188	1555	95	below_threshold
Salegentibacter echinorum	strain=DSM 24579	GCA_900129445.1	1073325	1073325	type	True	77.3727	231	1555	95	below_threshold
Antarcticibacterium arcticum	strain=PAMC 28998	GCA_007993795.1	2585771	2585771	type	True	76.9625	113	1555	95	below_threshold
Salinimicrobium marinum	strain=KCTC 12719	GCA_014651535.1	680283	680283	type	True	76.8478	154	1555	95	below_threshold
Haloflavibacter putidus	strain=PLHSN227	GCA_006546625.1	2576776	2576776	type	True	76.5671	116	1555	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.2388	83	1555	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.2094	103	1555	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:55,823] [INFO] DFAST Taxonomy check result was written to GCF_002094855.1_ASM209485v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:55,824] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:55,824] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:55,824] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19d3502a-e304-4f22-bce4-04f9a2709f47/dqc_reference/checkm_data
[2024-01-24 11:05:55,825] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:55,900] [INFO] Task started: CheckM
[2024-01-24 11:05:55,900] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002094855.1_ASM209485v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002094855.1_ASM209485v1_genomic.fna/checkm_input GCF_002094855.1_ASM209485v1_genomic.fna/checkm_result
[2024-01-24 11:06:40,981] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:40,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:41,011] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:41,011] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:41,012] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002094855.1_ASM209485v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:41,012] [INFO] Task started: Blastn
[2024-01-24 11:06:41,012] [INFO] Running command: blastn -query GCF_002094855.1_ASM209485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19d3502a-e304-4f22-bce4-04f9a2709f47/dqc_reference/reference_markers_gtdb.fasta -out GCF_002094855.1_ASM209485v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:41,957] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:41,966] [INFO] Selected 14 target genomes.
[2024-01-24 11:06:41,966] [INFO] Target genome list was writen to GCF_002094855.1_ASM209485v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:41,998] [INFO] Task started: fastANI
[2024-01-24 11:06:41,998] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d28d938-6b9c-41b8-a733-ee8150e0f3a7/GCF_002094855.1_ASM209485v1_genomic.fna.gz --refList GCF_002094855.1_ASM209485v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002094855.1_ASM209485v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:52,210] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:52,227] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:52,227] [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	100.0	1553	1555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zunongwangia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900112105.1	s__Zunongwangia mangrovi	91.5839	1157	1555	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	84.0861	1088	1555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zunongwangia	95.0	99.17	98.44	0.93	0.80	11	-
GCF_000423405.1	s__Mesonia mobilis	79.594	233	1555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.98	99.98	0.99	0.99	2	-
GCA_012964435.1	s__Mesonia sp012964435	78.9567	210	1555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900113135.1	s__Salegentibacter agarivorans	78.3157	327	1555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	97.64	95.65	0.87	0.86	4	-
GCF_900142975.1	s__Salegentibacter salegens	77.7182	288	1555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900168265.1	s__Salegentibacter salarius	77.5774	285	1555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	100.00	99.99	1.00	0.99	3	-
GCF_016236915.1	s__Salegentibacter maritimus	77.5644	247	1555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	98.25	98.21	0.91	0.91	3	-
GCF_900129445.1	s__Salegentibacter echinorum	77.3704	231	1555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105135.1	s__Gramella sp900105135	77.3246	215	1555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104765.1	s__Gillisia sp900104765	77.2211	196	1555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	98.23	98.23	0.92	0.92	2	-
GCF_014651535.1	s__Salinimicrobium marinum	76.8637	153	1555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003550275.1	s__QXCW01 sp003550275	76.8368	73	1555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__QXCW01	95.0	98.16	98.16	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:52,229] [INFO] GTDB search result was written to GCF_002094855.1_ASM209485v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:52,230] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:52,236] [INFO] DFAST_QC result json was written to GCF_002094855.1_ASM209485v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:52,236] [INFO] DFAST_QC completed!
[2024-01-24 11:06:52,236] [INFO] Total running time: 0h1m28s