[2024-01-24 13:01:38,049] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:38,051] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:38,052] [INFO] DQC Reference Directory: /var/lib/cwl/stg43acecf1-e88e-4a4d-a94f-dfc9259c2365/dqc_reference
[2024-01-24 13:01:40,903] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:40,904] [INFO] Task started: Prodigal
[2024-01-24 13:01:40,905] [INFO] Running command: gunzip -c /var/lib/cwl/stg6889fc9c-1e82-477b-b39a-2aa64f39c20f/GCF_000167355.1_ASM16735v1_genomic.fna.gz | prodigal -d GCF_000167355.1_ASM16735v1_genomic.fna/cds.fna -a GCF_000167355.1_ASM16735v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:52,593] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:52,593] [INFO] Task started: HMMsearch
[2024-01-24 13:01:52,593] [INFO] Running command: hmmsearch --tblout GCF_000167355.1_ASM16735v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43acecf1-e88e-4a4d-a94f-dfc9259c2365/dqc_reference/reference_markers.hmm GCF_000167355.1_ASM16735v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:52,864] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:52,865] [INFO] Found 6/6 markers.
[2024-01-24 13:01:52,906] [INFO] Query marker FASTA was written to GCF_000167355.1_ASM16735v1_genomic.fna/markers.fasta
[2024-01-24 13:01:52,907] [INFO] Task started: Blastn
[2024-01-24 13:01:52,907] [INFO] Running command: blastn -query GCF_000167355.1_ASM16735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43acecf1-e88e-4a4d-a94f-dfc9259c2365/dqc_reference/reference_markers.fasta -out GCF_000167355.1_ASM16735v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:53,636] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:53,640] [INFO] Selected 24 target genomes.
[2024-01-24 13:01:53,640] [INFO] Target genome list was writen to GCF_000167355.1_ASM16735v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:53,648] [INFO] Task started: fastANI
[2024-01-24 13:01:53,648] [INFO] Running command: fastANI --query /var/lib/cwl/stg6889fc9c-1e82-477b-b39a-2aa64f39c20f/GCF_000167355.1_ASM16735v1_genomic.fna.gz --refList GCF_000167355.1_ASM16735v1_genomic.fna/target_genomes.txt --output GCF_000167355.1_ASM16735v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:10,939] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:10,940] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43acecf1-e88e-4a4d-a94f-dfc9259c2365/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:10,940] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43acecf1-e88e-4a4d-a94f-dfc9259c2365/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:10,949] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:10,950] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:10,950] [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
Desulfuromonas acetoxidans	strain=DSM 684	GCA_000167355.1	891	891	type	True	100.0	1244	1247	95	conclusive
Desulfuromonas thiophila	strain=DSM 8987	GCA_900101955.1	57664	57664	type	True	77.6288	147	1247	95	below_threshold
Syntrophotalea carbinolica	strain=DSM 2380	GCA_000012885.1	19	19	type	True	77.0667	60	1247	95	below_threshold
Geoalkalibacter halelectricus	strain=SAP-1	GCA_025263685.1	2847045	2847045	type	True	76.8473	57	1247	95	below_threshold
Syntrophotalea acetylenivorans	strain=SFB93	GCA_001887775.1	1842532	1842532	type	True	76.5234	63	1247	95	below_threshold
Geothermobacter hydrogeniphilus	strain=EPR-M	GCA_002093115.1	1969733	1969733	type	True	76.3672	58	1247	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:10,959] [INFO] DFAST Taxonomy check result was written to GCF_000167355.1_ASM16735v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:10,960] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:10,960] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:10,960] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43acecf1-e88e-4a4d-a94f-dfc9259c2365/dqc_reference/checkm_data
[2024-01-24 13:02:10,962] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:11,022] [INFO] Task started: CheckM
[2024-01-24 13:02:11,023] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000167355.1_ASM16735v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000167355.1_ASM16735v1_genomic.fna/checkm_input GCF_000167355.1_ASM16735v1_genomic.fna/checkm_result
[2024-01-24 13:02:51,275] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:51,276] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.19%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:51,299] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:51,299] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:51,300] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000167355.1_ASM16735v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:51,300] [INFO] Task started: Blastn
[2024-01-24 13:02:51,300] [INFO] Running command: blastn -query GCF_000167355.1_ASM16735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43acecf1-e88e-4a4d-a94f-dfc9259c2365/dqc_reference/reference_markers_gtdb.fasta -out GCF_000167355.1_ASM16735v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:52,106] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:52,109] [INFO] Selected 24 target genomes.
[2024-01-24 13:02:52,110] [INFO] Target genome list was writen to GCF_000167355.1_ASM16735v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:52,131] [INFO] Task started: fastANI
[2024-01-24 13:02:52,131] [INFO] Running command: fastANI --query /var/lib/cwl/stg6889fc9c-1e82-477b-b39a-2aa64f39c20f/GCF_000167355.1_ASM16735v1_genomic.fna.gz --refList GCF_000167355.1_ASM16735v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000167355.1_ASM16735v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:06,665] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:06,681] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:06,681] [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_000167355.1	s__Desulfuromonas acetoxidans	100.0	1244	1247	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Desulfuromonadaceae;g__Desulfuromonas	95.0	99.97	99.95	0.96	0.96	4	conclusive
GCA_002869685.1	s__Desulfuromonas sp002869685	81.2553	523	1247	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Desulfuromonadaceae;g__Desulfuromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101955.1	s__Pseudodesulfuromonas thiophila	77.6498	147	1247	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Desulfuromonadaceae;g__Pseudodesulfuromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016936455.1	s__Pseudodesulfuromonas sp016936455	77.6013	160	1247	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Desulfuromonadaceae;g__Pseudodesulfuromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001751155.1	s__Desulfuromonas sp001751155	77.1469	72	1247	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Desulfuromonadaceae;g__Desulfuromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002084705.1	s__Desulfuromonas sp002084705	76.8192	74	1247	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Desulfuromonadaceae;g__Desulfuromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013152145.1	s__Malonomonas sp013152145	75.7708	50	1247	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geopsychrobacteraceae;g__Malonomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:06,683] [INFO] GTDB search result was written to GCF_000167355.1_ASM16735v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:06,684] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:06,688] [INFO] DFAST_QC result json was written to GCF_000167355.1_ASM16735v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:06,689] [INFO] DFAST_QC completed!
[2024-01-24 13:03:06,689] [INFO] Total running time: 0h1m29s