[2024-01-24 13:27:43,651] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:43,656] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:43,656] [INFO] DQC Reference Directory: /var/lib/cwl/stg2341dc46-d287-4e55-852b-c59589ce7631/dqc_reference
[2024-01-24 13:27:44,898] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:44,898] [INFO] Task started: Prodigal
[2024-01-24 13:27:44,899] [INFO] Running command: gunzip -c /var/lib/cwl/stgca651271-2a3c-4696-a3ee-817c569441c3/GCF_009208055.1_ASM920805v1_genomic.fna.gz | prodigal -d GCF_009208055.1_ASM920805v1_genomic.fna/cds.fna -a GCF_009208055.1_ASM920805v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:27:48,972] [INFO] Task succeeded: Prodigal
[2024-01-24 13:27:48,972] [INFO] Task started: HMMsearch
[2024-01-24 13:27:48,972] [INFO] Running command: hmmsearch --tblout GCF_009208055.1_ASM920805v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2341dc46-d287-4e55-852b-c59589ce7631/dqc_reference/reference_markers.hmm GCF_009208055.1_ASM920805v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:27:49,290] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:27:49,292] [INFO] Found 6/6 markers.
[2024-01-24 13:27:49,328] [INFO] Query marker FASTA was written to GCF_009208055.1_ASM920805v1_genomic.fna/markers.fasta
[2024-01-24 13:27:49,328] [INFO] Task started: Blastn
[2024-01-24 13:27:49,328] [INFO] Running command: blastn -query GCF_009208055.1_ASM920805v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2341dc46-d287-4e55-852b-c59589ce7631/dqc_reference/reference_markers.fasta -out GCF_009208055.1_ASM920805v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:50,030] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:50,033] [INFO] Selected 23 target genomes.
[2024-01-24 13:27:50,034] [INFO] Target genome list was writen to GCF_009208055.1_ASM920805v1_genomic.fna/target_genomes.txt
[2024-01-24 13:27:50,122] [INFO] Task started: fastANI
[2024-01-24 13:27:50,123] [INFO] Running command: fastANI --query /var/lib/cwl/stgca651271-2a3c-4696-a3ee-817c569441c3/GCF_009208055.1_ASM920805v1_genomic.fna.gz --refList GCF_009208055.1_ASM920805v1_genomic.fna/target_genomes.txt --output GCF_009208055.1_ASM920805v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:02,651] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:02,652] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2341dc46-d287-4e55-852b-c59589ce7631/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:02,652] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2341dc46-d287-4e55-852b-c59589ce7631/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:02,670] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:28:02,671] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:28:02,671] [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
Poseidonibacter lekithochrous	strain=DSM 100870	GCA_013283835.1	1904463	1904463	type	True	81.6236	542	886	95	below_threshold
Poseidonibacter lekithochrous	strain=LFT 1.7	GCA_001878855.1	1904463	1904463	type	True	81.4727	534	886	95	below_threshold
Arcobacter acticola	strain=KCTC 52212	GCA_013177675.1	1849015	1849015	type	True	80.9214	520	886	95	below_threshold
Malaciobacter pacificus	strain=CGMCC 1.11011	GCA_014636355.1	1080223	1080223	type	True	80.5455	453	886	95	below_threshold
Arcobacter venerupis	strain=LMG 26156	GCA_013201665.1	1054033	1054033	type	True	80.457	455	886	95	below_threshold
Malaciobacter pacificus	strain=LMG 26638	GCA_004214795.1	1080223	1080223	type	True	80.4436	461	886	95	below_threshold
Arcobacter aquimarinus	strain=CECT 8442	GCA_004115795.1	1315211	1315211	type	True	80.3515	414	886	95	below_threshold
Arcobacter ellisii	strain=LMG 26155	GCA_003544915.1	913109	913109	type	True	80.3288	451	886	95	below_threshold
Arcobacter venerupis	strain=CECT7836	GCA_004023405.1	1054033	1054033	type	True	80.327	455	886	95	below_threshold
Arcobacter ellisii	strain=CECT 7837	GCA_004115815.1	913109	913109	type	True	80.3228	450	886	95	below_threshold
Arcobacter suis	strain=CECT7833	GCA_004023465.1	1278212	1278212	type	True	80.1658	426	886	95	below_threshold
Arcobacter suis	strain=CECT 7833	GCA_003544815.1	1278212	1278212	type	True	80.1599	430	886	95	below_threshold
Arcobacter aquimarinus	strain=W63	GCA_013177635.1	1315211	1315211	type	True	80.1296	433	886	95	below_threshold
Arcobacter cloacae	strain=CECT 7834	GCA_004115805.1	1054034	1054034	type	True	80.0622	423	886	95	below_threshold
Arcobacter defluvii	strain=LMG 25694	GCA_013201725.1	873191	873191	type	True	80.0513	450	886	95	below_threshold
Arcobacter defluvii	strain=CECT 7697	GCA_004115775.1	873191	873191	type	True	80.0001	443	886	95	below_threshold
[Halarcobacter] arenosus	strain=CAU 1517	GCA_005771535.1	2576037	2576037	type	True	79.1324	407	886	95	below_threshold
Malaciobacter molluscorum	strain=F98-3	GCA_002701265.1	1032072	1032072	type	True	79.0	365	886	95	below_threshold
Malaciobacter halophilus	strain=DSM 18005	GCA_002837275.1	197482	197482	type	True	78.9116	365	886	95	below_threshold
Malaciobacter molluscorum	strain=CECT 7696	GCA_003544935.1	1032072	1032072	type	True	78.8862	388	886	95	below_threshold
Aliarcobacter faecis	strain=LMG 28519	GCA_024584135.1	1564138	1564138	type	True	78.5423	297	886	95	below_threshold
Arcobacter vandammei	strain=R-73987	GCA_016106035.1	2782243	2782243	type	True	78.4607	284	886	95	below_threshold
Arcobacter vandammei	strain=LMG 31429	GCA_024583975.1	2782243	2782243	type	True	78.4048	290	886	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:02,673] [INFO] DFAST Taxonomy check result was written to GCF_009208055.1_ASM920805v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:02,674] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:02,674] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:02,674] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2341dc46-d287-4e55-852b-c59589ce7631/dqc_reference/checkm_data
[2024-01-24 13:28:02,676] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:02,707] [INFO] Task started: CheckM
[2024-01-24 13:28:02,707] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009208055.1_ASM920805v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009208055.1_ASM920805v1_genomic.fna/checkm_input GCF_009208055.1_ASM920805v1_genomic.fna/checkm_result
[2024-01-24 13:28:23,852] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:23,853] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:23,875] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:23,875] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:23,876] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009208055.1_ASM920805v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:23,876] [INFO] Task started: Blastn
[2024-01-24 13:28:23,876] [INFO] Running command: blastn -query GCF_009208055.1_ASM920805v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2341dc46-d287-4e55-852b-c59589ce7631/dqc_reference/reference_markers_gtdb.fasta -out GCF_009208055.1_ASM920805v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:24,969] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:24,973] [INFO] Selected 8 target genomes.
[2024-01-24 13:28:24,973] [INFO] Target genome list was writen to GCF_009208055.1_ASM920805v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:24,985] [INFO] Task started: fastANI
[2024-01-24 13:28:24,986] [INFO] Running command: fastANI --query /var/lib/cwl/stgca651271-2a3c-4696-a3ee-817c569441c3/GCF_009208055.1_ASM920805v1_genomic.fna.gz --refList GCF_009208055.1_ASM920805v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009208055.1_ASM920805v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:30,263] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:30,271] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:30,271] [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_009208075.1	s__Poseidonibacter sp009208075	99.6252	830	886	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	99.63	99.63	0.93	0.93	3	conclusive
GCF_018861145.1	s__Poseidonibacter lekithochrous_A	87.3455	655	886	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002685075.1	s__Poseidonibacter sp002685075	87.3208	558	886	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479135.1	s__Poseidonibacter sp905479135	87.1558	410	886	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956695.1	s__Poseidonibacter parvus	85.312	649	886	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	98.33	98.33	0.91	0.91	2	-
GCF_003667345.1	s__Poseidonibacter antarcticus	83.7356	583	886	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013201935.1	s__Aliarcobacter cloacae	79.9751	436	886	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.96	95.91	0.93	0.87	3	-
GCF_003660105.1	s__Aliarcobacter cryaerophilus	78.4646	290	886	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.99	99.99	1.00	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:28:30,273] [INFO] GTDB search result was written to GCF_009208055.1_ASM920805v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:30,273] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:30,278] [INFO] DFAST_QC result json was written to GCF_009208055.1_ASM920805v1_genomic.fna/dqc_result.json
[2024-01-24 13:28:30,278] [INFO] DFAST_QC completed!
[2024-01-24 13:28:30,278] [INFO] Total running time: 0h0m47s