[2024-01-25 20:05:50,506] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:05:50,511] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:05:50,511] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e956980-c4a2-4981-b7c6-cf3c4bd44a73/dqc_reference
[2024-01-25 20:05:51,707] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:05:51,708] [INFO] Task started: Prodigal
[2024-01-25 20:05:51,708] [INFO] Running command: gunzip -c /var/lib/cwl/stg600f4115-3460-4afc-9bb8-efc1bd70ee10/GCF_003544855.1_ASM354485v1_genomic.fna.gz | prodigal -d GCF_003544855.1_ASM354485v1_genomic.fna/cds.fna -a GCF_003544855.1_ASM354485v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:05:55,835] [INFO] Task succeeded: Prodigal
[2024-01-25 20:05:55,835] [INFO] Task started: HMMsearch
[2024-01-25 20:05:55,835] [INFO] Running command: hmmsearch --tblout GCF_003544855.1_ASM354485v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e956980-c4a2-4981-b7c6-cf3c4bd44a73/dqc_reference/reference_markers.hmm GCF_003544855.1_ASM354485v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:05:56,031] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:05:56,032] [INFO] Found 6/6 markers.
[2024-01-25 20:05:56,057] [INFO] Query marker FASTA was written to GCF_003544855.1_ASM354485v1_genomic.fna/markers.fasta
[2024-01-25 20:05:56,058] [INFO] Task started: Blastn
[2024-01-25 20:05:56,058] [INFO] Running command: blastn -query GCF_003544855.1_ASM354485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e956980-c4a2-4981-b7c6-cf3c4bd44a73/dqc_reference/reference_markers.fasta -out GCF_003544855.1_ASM354485v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:56,686] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:56,688] [INFO] Selected 7 target genomes.
[2024-01-25 20:05:56,689] [INFO] Target genome list was writen to GCF_003544855.1_ASM354485v1_genomic.fna/target_genomes.txt
[2024-01-25 20:05:56,697] [INFO] Task started: fastANI
[2024-01-25 20:05:56,697] [INFO] Running command: fastANI --query /var/lib/cwl/stg600f4115-3460-4afc-9bb8-efc1bd70ee10/GCF_003544855.1_ASM354485v1_genomic.fna.gz --refList GCF_003544855.1_ASM354485v1_genomic.fna/target_genomes.txt --output GCF_003544855.1_ASM354485v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:06:01,746] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:01,747] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e956980-c4a2-4981-b7c6-cf3c4bd44a73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:06:01,747] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e956980-c4a2-4981-b7c6-cf3c4bd44a73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:06:01,755] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 20:06:01,755] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 20:06:01,755] [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
Malaciobacter marinus	strain=JCM 15502	GCA_003544855.1	505249	505249	type	True	100.0	970	972	95	inconclusive
Malaciobacter canalis	strain=LMG 29148	GCA_008000835.1	1912871	1912871	type	True	95.4946	840	972	95	inconclusive
Malaciobacter canalis	strain=F138-33	GCA_002723485.1	1912871	1912871	type	True	95.4231	807	972	95	inconclusive
Malaciobacter halophilus	strain=DSM 18005	GCA_002837275.1	197482	197482	type	True	87.323	760	972	95	below_threshold
Malaciobacter mytili	strain=LMG 24559	GCA_003346775.1	603050	603050	type	True	82.3642	644	972	95	below_threshold
Malaciobacter mytili	strain=CECT 7386	GCA_004116555.1	603050	603050	type	True	82.1847	630	972	95	below_threshold
Malaciobacter molluscorum	strain=CECT 7696	GCA_003544935.1	1032072	1032072	type	True	82.1172	629	972	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:06:01,756] [INFO] DFAST Taxonomy check result was written to GCF_003544855.1_ASM354485v1_genomic.fna/tc_result.tsv
[2024-01-25 20:06:01,757] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:06:01,757] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:06:01,757] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e956980-c4a2-4981-b7c6-cf3c4bd44a73/dqc_reference/checkm_data
[2024-01-25 20:06:01,758] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:06:01,787] [INFO] Task started: CheckM
[2024-01-25 20:06:01,787] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003544855.1_ASM354485v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003544855.1_ASM354485v1_genomic.fna/checkm_input GCF_003544855.1_ASM354485v1_genomic.fna/checkm_result
[2024-01-25 20:06:20,551] [INFO] Task succeeded: CheckM
[2024-01-25 20:06:20,552] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:06:20,580] [INFO] ===== Completeness check finished =====
[2024-01-25 20:06:20,580] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:06:20,580] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003544855.1_ASM354485v1_genomic.fna/markers.fasta)
[2024-01-25 20:06:20,581] [INFO] Task started: Blastn
[2024-01-25 20:06:20,581] [INFO] Running command: blastn -query GCF_003544855.1_ASM354485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e956980-c4a2-4981-b7c6-cf3c4bd44a73/dqc_reference/reference_markers_gtdb.fasta -out GCF_003544855.1_ASM354485v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:06:21,545] [INFO] Task succeeded: Blastn
[2024-01-25 20:06:21,548] [INFO] Selected 7 target genomes.
[2024-01-25 20:06:21,548] [INFO] Target genome list was writen to GCF_003544855.1_ASM354485v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:06:21,563] [INFO] Task started: fastANI
[2024-01-25 20:06:21,563] [INFO] Running command: fastANI --query /var/lib/cwl/stg600f4115-3460-4afc-9bb8-efc1bd70ee10/GCF_003544855.1_ASM354485v1_genomic.fna.gz --refList GCF_003544855.1_ASM354485v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003544855.1_ASM354485v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:06:26,703] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:26,709] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:06:26,709] [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_003544855.1	s__Malaciobacter marinus	100.0	970	972	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	98.03	95.41	0.91	0.86	14	conclusive
GCF_002837275.1	s__Malaciobacter halophilus	87.323	760	972	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003346775.1	s__Malaciobacter mytili	82.321	644	972	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	99.45	98.91	0.96	0.92	3	-
GCF_003544935.1	s__Malaciobacter molluscorum	82.1703	628	972	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	99.44	98.88	0.96	0.91	3	-
GCA_004116495.1	s__Malaciobacter sp004116495	81.9975	602	972	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004116725.1	s__Malaciobacter sp004116725	81.9438	602	972	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667345.1	s__Poseidonibacter antarcticus	78.7198	384	972	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:06:26,711] [INFO] GTDB search result was written to GCF_003544855.1_ASM354485v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:06:26,711] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:06:26,714] [INFO] DFAST_QC result json was written to GCF_003544855.1_ASM354485v1_genomic.fna/dqc_result.json
[2024-01-25 20:06:26,714] [INFO] DFAST_QC completed!
[2024-01-25 20:06:26,714] [INFO] Total running time: 0h0m36s