[2024-01-24 11:26:26,140] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:26,142] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:26,143] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d1ca683-f992-4919-bcd2-57255ead83f9/dqc_reference
[2024-01-24 11:26:27,423] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:27,424] [INFO] Task started: Prodigal
[2024-01-24 11:26:27,425] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa5877d9-0fda-469c-8676-40101b8d7a04/GCF_017338855.1_ASM1733885v1_genomic.fna.gz | prodigal -d GCF_017338855.1_ASM1733885v1_genomic.fna/cds.fna -a GCF_017338855.1_ASM1733885v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:38,281] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:38,282] [INFO] Task started: HMMsearch
[2024-01-24 11:26:38,282] [INFO] Running command: hmmsearch --tblout GCF_017338855.1_ASM1733885v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d1ca683-f992-4919-bcd2-57255ead83f9/dqc_reference/reference_markers.hmm GCF_017338855.1_ASM1733885v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:38,581] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:38,583] [INFO] Found 6/6 markers.
[2024-01-24 11:26:38,615] [INFO] Query marker FASTA was written to GCF_017338855.1_ASM1733885v1_genomic.fna/markers.fasta
[2024-01-24 11:26:38,616] [INFO] Task started: Blastn
[2024-01-24 11:26:38,616] [INFO] Running command: blastn -query GCF_017338855.1_ASM1733885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d1ca683-f992-4919-bcd2-57255ead83f9/dqc_reference/reference_markers.fasta -out GCF_017338855.1_ASM1733885v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:39,314] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:39,317] [INFO] Selected 9 target genomes.
[2024-01-24 11:26:39,317] [INFO] Target genome list was writen to GCF_017338855.1_ASM1733885v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:39,322] [INFO] Task started: fastANI
[2024-01-24 11:26:39,322] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa5877d9-0fda-469c-8676-40101b8d7a04/GCF_017338855.1_ASM1733885v1_genomic.fna.gz --refList GCF_017338855.1_ASM1733885v1_genomic.fna/target_genomes.txt --output GCF_017338855.1_ASM1733885v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:47,049] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:47,050] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d1ca683-f992-4919-bcd2-57255ead83f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:47,050] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d1ca683-f992-4919-bcd2-57255ead83f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:47,057] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:47,057] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:47,058] [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 benzoatilyticus	strain=Jerry-YX	GCA_017338855.1	2815309	2815309	type	True	100.0	1194	1194	95	conclusive
Geobacter grbiciae	strain=DSM 13689	GCA_018531165.1	155042	155042	type	True	83.3024	756	1194	95	below_threshold
Geobacter metallireducens	strain=GS-15	GCA_000012925.1	28232	28232	type	True	83.2421	750	1194	95	below_threshold
Geobacter hydrogenophilus	strain=DSM 13691	GCA_018501225.1	40983	40983	type	True	83.0536	744	1194	95	below_threshold
Geobacter pickeringii	strain=G13	GCA_000817955.1	345632	345632	type	True	80.5239	491	1194	95	below_threshold
Geobacter sulfurreducens	strain=PCA	GCA_000007985.2	35554	35554	type	True	80.0518	483	1194	95	below_threshold
Pelobacter propionicus	strain=DSM 2379	GCA_000015045.1	29543	29543	type	True	77.772	176	1194	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:47,059] [INFO] DFAST Taxonomy check result was written to GCF_017338855.1_ASM1733885v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:47,060] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:47,060] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:47,060] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d1ca683-f992-4919-bcd2-57255ead83f9/dqc_reference/checkm_data
[2024-01-24 11:26:47,061] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:47,097] [INFO] Task started: CheckM
[2024-01-24 11:26:47,097] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017338855.1_ASM1733885v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017338855.1_ASM1733885v1_genomic.fna/checkm_input GCF_017338855.1_ASM1733885v1_genomic.fna/checkm_result
[2024-01-24 11:27:23,318] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:23,319] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.24%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:23,336] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:23,337] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:23,337] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017338855.1_ASM1733885v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:23,338] [INFO] Task started: Blastn
[2024-01-24 11:27:23,338] [INFO] Running command: blastn -query GCF_017338855.1_ASM1733885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d1ca683-f992-4919-bcd2-57255ead83f9/dqc_reference/reference_markers_gtdb.fasta -out GCF_017338855.1_ASM1733885v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:24,311] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:24,315] [INFO] Selected 13 target genomes.
[2024-01-24 11:27:24,315] [INFO] Target genome list was writen to GCF_017338855.1_ASM1733885v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:24,343] [INFO] Task started: fastANI
[2024-01-24 11:27:24,343] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa5877d9-0fda-469c-8676-40101b8d7a04/GCF_017338855.1_ASM1733885v1_genomic.fna.gz --refList GCF_017338855.1_ASM1733885v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017338855.1_ASM1733885v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:34,018] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:34,033] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:34,033] [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_017338855.1	s__Geobacter sp017338855	100.0	1193	1194	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011046855.1	s__Geobacter metallireducens_A	83.5116	668	1194	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	83.238	751	1194	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	98.29	96.59	0.93	0.85	3	-
GCF_018501225.1	s__Geobacter hydrogenophilus	83.0598	743	1194	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	82.4718	437	1194	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001628815.1	s__Geobacter anodireducens	80.4137	493	1194	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	99.35	99.24	0.91	0.90	4	-
GCF_000007985.2	s__Geobacter sulfurreducens	80.0306	482	1194	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	98.43	95.82	0.96	0.94	8	-
GCF_003053505.1	s__RPRC01 sp003053505	78.1875	140	1194	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__RPRC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003574885.1	s__Geomobilimonas sp003574885	77.8582	251	1194	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomobilimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903857795.1	s__CAIOGM01 sp903857795	77.7064	184	1194	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__CAIOGM01;g__CAIOGM01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:34,035] [INFO] GTDB search result was written to GCF_017338855.1_ASM1733885v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:34,036] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:34,039] [INFO] DFAST_QC result json was written to GCF_017338855.1_ASM1733885v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:34,040] [INFO] DFAST_QC completed!
[2024-01-24 11:27:34,040] [INFO] Total running time: 0h1m8s