[2024-01-24 13:27:59,299] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:59,301] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:59,301] [INFO] DQC Reference Directory: /var/lib/cwl/stg8048d346-7f4d-4d60-a73e-a1ba3cf32dcb/dqc_reference
[2024-01-24 13:28:00,529] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:00,530] [INFO] Task started: Prodigal
[2024-01-24 13:28:00,530] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ad6c3bc-c4f8-4ad8-b7e2-4d64fa45a30d/GCF_000007985.2_ASM798v2_genomic.fna.gz | prodigal -d GCF_000007985.2_ASM798v2_genomic.fna/cds.fna -a GCF_000007985.2_ASM798v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:12,483] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:12,483] [INFO] Task started: HMMsearch
[2024-01-24 13:28:12,483] [INFO] Running command: hmmsearch --tblout GCF_000007985.2_ASM798v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8048d346-7f4d-4d60-a73e-a1ba3cf32dcb/dqc_reference/reference_markers.hmm GCF_000007985.2_ASM798v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:12,720] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:12,721] [INFO] Found 6/6 markers.
[2024-01-24 13:28:12,753] [INFO] Query marker FASTA was written to GCF_000007985.2_ASM798v2_genomic.fna/markers.fasta
[2024-01-24 13:28:12,753] [INFO] Task started: Blastn
[2024-01-24 13:28:12,753] [INFO] Running command: blastn -query GCF_000007985.2_ASM798v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8048d346-7f4d-4d60-a73e-a1ba3cf32dcb/dqc_reference/reference_markers.fasta -out GCF_000007985.2_ASM798v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:13,416] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:13,419] [INFO] Selected 7 target genomes.
[2024-01-24 13:28:13,420] [INFO] Target genome list was writen to GCF_000007985.2_ASM798v2_genomic.fna/target_genomes.txt
[2024-01-24 13:28:13,424] [INFO] Task started: fastANI
[2024-01-24 13:28:13,424] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ad6c3bc-c4f8-4ad8-b7e2-4d64fa45a30d/GCF_000007985.2_ASM798v2_genomic.fna.gz --refList GCF_000007985.2_ASM798v2_genomic.fna/target_genomes.txt --output GCF_000007985.2_ASM798v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:19,398] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:19,398] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8048d346-7f4d-4d60-a73e-a1ba3cf32dcb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:19,399] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8048d346-7f4d-4d60-a73e-a1ba3cf32dcb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:19,406] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:19,407] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:19,407] [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
Geobacter sulfurreducens	strain=PCA	GCA_000007985.2	35554	35554	type	True	100.0	1270	1271	95	conclusive
Geobacter soli	strain=GSS01	GCA_000816575.1	1510391	1510391	type	True	92.6873	1033	1271	95	below_threshold
Geobacter hydrogenophilus	strain=DSM 13691	GCA_018501225.1	40983	40983	type	True	80.5794	583	1271	95	below_threshold
Geobacter pickeringii	strain=G13	GCA_000817955.1	345632	345632	type	True	80.5534	528	1271	95	below_threshold
Geobacter grbiciae	strain=DSM 13689	GCA_018531165.1	155042	155042	type	True	80.4775	570	1271	95	below_threshold
Geobacter metallireducens	strain=GS-15	GCA_000012925.1	28232	28232	type	True	80.3589	568	1271	95	below_threshold
Geobacter benzoatilyticus	strain=Jerry-YX	GCA_017338855.1	2815309	2815309	type	True	80.1267	476	1271	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:19,408] [INFO] DFAST Taxonomy check result was written to GCF_000007985.2_ASM798v2_genomic.fna/tc_result.tsv
[2024-01-24 13:28:19,411] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:19,411] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:19,411] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8048d346-7f4d-4d60-a73e-a1ba3cf32dcb/dqc_reference/checkm_data
[2024-01-24 13:28:19,412] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:19,451] [INFO] Task started: CheckM
[2024-01-24 13:28:19,451] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000007985.2_ASM798v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000007985.2_ASM798v2_genomic.fna/checkm_input GCF_000007985.2_ASM798v2_genomic.fna/checkm_result
[2024-01-24 13:28:56,007] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:56,008] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:56,032] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:56,032] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:56,033] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000007985.2_ASM798v2_genomic.fna/markers.fasta)
[2024-01-24 13:28:56,033] [INFO] Task started: Blastn
[2024-01-24 13:28:56,033] [INFO] Running command: blastn -query GCF_000007985.2_ASM798v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8048d346-7f4d-4d60-a73e-a1ba3cf32dcb/dqc_reference/reference_markers_gtdb.fasta -out GCF_000007985.2_ASM798v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:56,974] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:56,977] [INFO] Selected 8 target genomes.
[2024-01-24 13:28:56,977] [INFO] Target genome list was writen to GCF_000007985.2_ASM798v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:56,987] [INFO] Task started: fastANI
[2024-01-24 13:28:56,987] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ad6c3bc-c4f8-4ad8-b7e2-4d64fa45a30d/GCF_000007985.2_ASM798v2_genomic.fna.gz --refList GCF_000007985.2_ASM798v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000007985.2_ASM798v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:03,068] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:03,076] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:03,076] [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_000007985.2	s__Geobacter sulfurreducens	100.0	1271	1271	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	98.43	95.82	0.96	0.94	8	conclusive
GCA_001628815.1	s__Geobacter anodireducens	92.6327	1042	1271	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	99.35	99.24	0.91	0.90	4	-
GCA_011046855.1	s__Geobacter metallireducens_A	81.0766	603	1271	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018501225.1	s__Geobacter hydrogenophilus	80.552	585	1271	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000817955.1	s__Geobacter pickeringii	80.5062	531	1271	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012925.1	s__Geobacter metallireducens	80.3309	571	1271	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	98.29	96.59	0.93	0.85	3	-
GCF_017338855.1	s__Geobacter sp017338855	80.1044	478	1271	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905339345.1	s__Geobacter sp905339345	79.9956	353	1271	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:03,088] [INFO] GTDB search result was written to GCF_000007985.2_ASM798v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:03,089] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:03,092] [INFO] DFAST_QC result json was written to GCF_000007985.2_ASM798v2_genomic.fna/dqc_result.json
[2024-01-24 13:29:03,092] [INFO] DFAST_QC completed!
[2024-01-24 13:29:03,092] [INFO] Total running time: 0h1m4s