[2024-01-24 13:12:38,883] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:38,887] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:38,889] [INFO] DQC Reference Directory: /var/lib/cwl/stgd213135c-4a2f-424c-ae3d-f09adcd940d3/dqc_reference
[2024-01-24 13:12:40,274] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:40,275] [INFO] Task started: Prodigal
[2024-01-24 13:12:40,275] [INFO] Running command: gunzip -c /var/lib/cwl/stg31627b23-2468-4a26-9fc2-920d15f20024/GCF_004116675.1_ASM411667v1_genomic.fna.gz | prodigal -d GCF_004116675.1_ASM411667v1_genomic.fna/cds.fna -a GCF_004116675.1_ASM411667v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:12:44,389] [INFO] Task succeeded: Prodigal
[2024-01-24 13:12:44,389] [INFO] Task started: HMMsearch
[2024-01-24 13:12:44,390] [INFO] Running command: hmmsearch --tblout GCF_004116675.1_ASM411667v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd213135c-4a2f-424c-ae3d-f09adcd940d3/dqc_reference/reference_markers.hmm GCF_004116675.1_ASM411667v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:12:44,707] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:12:44,708] [INFO] Found 6/6 markers.
[2024-01-24 13:12:44,737] [INFO] Query marker FASTA was written to GCF_004116675.1_ASM411667v1_genomic.fna/markers.fasta
[2024-01-24 13:12:44,738] [INFO] Task started: Blastn
[2024-01-24 13:12:44,738] [INFO] Running command: blastn -query GCF_004116675.1_ASM411667v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd213135c-4a2f-424c-ae3d-f09adcd940d3/dqc_reference/reference_markers.fasta -out GCF_004116675.1_ASM411667v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:45,382] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:45,385] [INFO] Selected 21 target genomes.
[2024-01-24 13:12:45,385] [INFO] Target genome list was writen to GCF_004116675.1_ASM411667v1_genomic.fna/target_genomes.txt
[2024-01-24 13:12:45,733] [INFO] Task started: fastANI
[2024-01-24 13:12:45,733] [INFO] Running command: fastANI --query /var/lib/cwl/stg31627b23-2468-4a26-9fc2-920d15f20024/GCF_004116675.1_ASM411667v1_genomic.fna.gz --refList GCF_004116675.1_ASM411667v1_genomic.fna/target_genomes.txt --output GCF_004116675.1_ASM411667v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:12:57,650] [INFO] Task succeeded: fastANI
[2024-01-24 13:12:57,650] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd213135c-4a2f-424c-ae3d-f09adcd940d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:12:57,651] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd213135c-4a2f-424c-ae3d-f09adcd940d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:12:57,675] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:12:57,675] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:12:57,675] [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
Halarcobacter bivalviorum	strain=CECT 7835	GCA_004116675.1	663364	663364	type	True	100.0	877	878	95	conclusive
Halarcobacter bivalviorum	strain=LMG 26154	GCA_003346815.1	663364	663364	type	True	99.9997	878	878	95	conclusive
[Halarcobacter] arenosus	strain=CAU 1517	GCA_005771535.1	2576037	2576037	type	True	80.667	476	878	95	below_threshold
Malaciobacter mytili	strain=LMG 24559	GCA_003346775.1	603050	603050	type	True	80.2464	506	878	95	below_threshold
Malaciobacter mytili	strain=CECT 7386	GCA_004116555.1	603050	603050	type	True	80.2303	491	878	95	below_threshold
Malaciobacter pacificus	strain=LMG 26638	GCA_004214795.1	1080223	1080223	type	True	80.2122	401	878	95	below_threshold
Malaciobacter pacificus	strain=CGMCC 1.11011	GCA_014636355.1	1080223	1080223	type	True	80.0911	408	878	95	below_threshold
Malaciobacter halophilus	strain=DSM 18005	GCA_002837275.1	197482	197482	type	True	79.973	461	878	95	below_threshold
Halarcobacter ebronensis	strain=CECT 8441	GCA_004116565.1	1462615	1462615	type	True	79.9524	469	878	95	below_threshold
Halarcobacter ebronensis	strain=LMG 27922	GCA_013201825.1	1462615	1462615	type	True	79.9283	473	878	95	below_threshold
Arcobacter ellisii	strain=CECT 7837	GCA_004115815.1	913109	913109	type	True	79.6338	415	878	95	below_threshold
Arcobacter ellisii	strain=LMG 26155	GCA_003544915.1	913109	913109	type	True	79.5399	414	878	95	below_threshold
Malaciobacter molluscorum	strain=CECT 7696	GCA_003544935.1	1032072	1032072	type	True	79.4914	409	878	95	below_threshold
Halarcobacter anaerophilus	strain=DSM 24636	GCA_004116345.1	877500	877500	type	True	79.0225	402	878	95	below_threshold
Halarcobacter anaerophilus	strain=DSM 24636	GCA_006459125.1	877500	877500	type	True	79.0142	407	878	95	below_threshold
Arcobacter nitrofigilis	strain=DSM 7299	GCA_000092245.1	28199	28199	type	True	78.9954	392	878	95	below_threshold
Aliarcobacter skirrowii	strain=CCUG 10374	GCA_003544835.1	28200	28200	type	True	78.5826	275	878	95	below_threshold
Aliarcobacter skirrowii	strain=LMG 6621	GCA_004115735.1	28200	28200	type	True	78.5348	277	878	95	below_threshold
Aliarcobacter skirrowii	strain=LMG 6621	GCA_024584055.1	28200	28200	type	True	78.5214	282	878	95	below_threshold
Aliarcobacter skirrowii	strain=CCUG 10374	GCA_008802155.1	28200	28200	type	True	78.5005	281	878	95	below_threshold
Aliarcobacter skirrowii	strain=NCTC12713	GCA_900445295.1	28200	28200	type	True	78.4834	280	878	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:12:57,678] [INFO] DFAST Taxonomy check result was written to GCF_004116675.1_ASM411667v1_genomic.fna/tc_result.tsv
[2024-01-24 13:12:57,679] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:12:57,680] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:12:57,680] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd213135c-4a2f-424c-ae3d-f09adcd940d3/dqc_reference/checkm_data
[2024-01-24 13:12:57,681] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:12:57,709] [INFO] Task started: CheckM
[2024-01-24 13:12:57,710] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004116675.1_ASM411667v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004116675.1_ASM411667v1_genomic.fna/checkm_input GCF_004116675.1_ASM411667v1_genomic.fna/checkm_result
[2024-01-24 13:13:19,143] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:19,144] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.78%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2024-01-24 13:13:19,167] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:19,168] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:19,168] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004116675.1_ASM411667v1_genomic.fna/markers.fasta)
[2024-01-24 13:13:19,169] [INFO] Task started: Blastn
[2024-01-24 13:13:19,169] [INFO] Running command: blastn -query GCF_004116675.1_ASM411667v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd213135c-4a2f-424c-ae3d-f09adcd940d3/dqc_reference/reference_markers_gtdb.fasta -out GCF_004116675.1_ASM411667v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:20,125] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:20,128] [INFO] Selected 13 target genomes.
[2024-01-24 13:13:20,128] [INFO] Target genome list was writen to GCF_004116675.1_ASM411667v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:20,142] [INFO] Task started: fastANI
[2024-01-24 13:13:20,142] [INFO] Running command: fastANI --query /var/lib/cwl/stg31627b23-2468-4a26-9fc2-920d15f20024/GCF_004116675.1_ASM411667v1_genomic.fna.gz --refList GCF_004116675.1_ASM411667v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004116675.1_ASM411667v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:13:27,374] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:27,392] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:13:27,392] [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_003346815.1	s__Halarcobacter bivalviorum	99.9997	878	878	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	98.23	96.46	0.96	0.92	3	conclusive
GCA_004116455.1	s__Halarcobacter sp004116455	86.4178	720	878	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	96.86	96.86	0.84	0.84	2	-
GCA_004118855.1	s__Halarcobacter sp004118855	85.4451	684	878	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373175.1	s__Halarcobacter sp013373175	85.2352	690	878	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004116625.1	s__Halarcobacter mediterraneus	83.0262	603	878	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001895145.1	s__Halarcobacter sp001895145	80.647	478	878	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003252105.1	s__Halarcobacter sp003252105	80.3072	431	878	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003346775.1	s__Malaciobacter mytili	80.2673	506	878	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	99.45	98.91	0.96	0.92	3	-
GCF_003544835.1	s__Aliarcobacter skirrowii	78.6054	273	878	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.32	95.07	0.91	0.85	16	-
GCF_004299785.2	s__Aliarcobacter porcinus	78.6041	268	878	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.76	98.06	0.91	0.88	6	-
GCA_017996075.1	s__Aliarcobacter sp017996075	78.4976	138	878	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.83	97.42	0.84	0.83	6	-
GCF_016106035.1	s__Aliarcobacter sp016106035	78.4363	275	878	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004214815.1	s__Aliarcobacter thereius	78.4064	279	878	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.14	98.62	0.93	0.89	8	-
--------------------------------------------------------------------------------
[2024-01-24 13:13:27,394] [INFO] GTDB search result was written to GCF_004116675.1_ASM411667v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:13:27,394] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:13:27,398] [INFO] DFAST_QC result json was written to GCF_004116675.1_ASM411667v1_genomic.fna/dqc_result.json
[2024-01-24 13:13:27,399] [INFO] DFAST_QC completed!
[2024-01-24 13:13:27,399] [INFO] Total running time: 0h0m49s