[2024-01-25 20:04:20,748] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:04:20,749] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:04:20,749] [INFO] DQC Reference Directory: /var/lib/cwl/stg57473330-d6a9-4829-80ec-696a6e37d4ca/dqc_reference
[2024-01-25 20:04:21,870] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:04:21,870] [INFO] Task started: Prodigal
[2024-01-25 20:04:21,871] [INFO] Running command: gunzip -c /var/lib/cwl/stgf289b40b-6b66-46d5-bdf4-29cca0846567/GCF_002197845.1_ASM219784v1_genomic.fna.gz | prodigal -d GCF_002197845.1_ASM219784v1_genomic.fna/cds.fna -a GCF_002197845.1_ASM219784v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:04:56,093] [INFO] Task succeeded: Prodigal
[2024-01-25 20:04:56,093] [INFO] Task started: HMMsearch
[2024-01-25 20:04:56,093] [INFO] Running command: hmmsearch --tblout GCF_002197845.1_ASM219784v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57473330-d6a9-4829-80ec-696a6e37d4ca/dqc_reference/reference_markers.hmm GCF_002197845.1_ASM219784v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:04:56,518] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:04:56,519] [INFO] Found 6/6 markers.
[2024-01-25 20:04:56,604] [INFO] Query marker FASTA was written to GCF_002197845.1_ASM219784v1_genomic.fna/markers.fasta
[2024-01-25 20:04:56,605] [INFO] Task started: Blastn
[2024-01-25 20:04:56,605] [INFO] Running command: blastn -query GCF_002197845.1_ASM219784v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57473330-d6a9-4829-80ec-696a6e37d4ca/dqc_reference/reference_markers.fasta -out GCF_002197845.1_ASM219784v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:57,182] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:57,185] [INFO] Selected 12 target genomes.
[2024-01-25 20:04:57,185] [INFO] Target genome list was writen to GCF_002197845.1_ASM219784v1_genomic.fna/target_genomes.txt
[2024-01-25 20:04:57,205] [INFO] Task started: fastANI
[2024-01-25 20:04:57,205] [INFO] Running command: fastANI --query /var/lib/cwl/stgf289b40b-6b66-46d5-bdf4-29cca0846567/GCF_002197845.1_ASM219784v1_genomic.fna.gz --refList GCF_002197845.1_ASM219784v1_genomic.fna/target_genomes.txt --output GCF_002197845.1_ASM219784v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:05:21,191] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:21,191] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57473330-d6a9-4829-80ec-696a6e37d4ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:05:21,192] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57473330-d6a9-4829-80ec-696a6e37d4ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:05:21,200] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:05:21,200] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:05:21,201] [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
Fimbriiglobus ruber	strain=SP5	GCA_002197845.1	1908690	1908690	type	True	100.0	4097	4108	95	conclusive
Limnoglobus roseus	strain=PX52	GCA_008254045.1	2598579	2598579	type	True	76.9636	755	4108	95	below_threshold
Urbifossiella limnaea	strain=ETA_A1	GCA_007747215.1	2528023	2528023	type	True	76.7741	796	4108	95	below_threshold
Gemmata obscuriglobus	strain=DSM 5831	GCA_008065095.1	114	114	type	True	76.6111	651	4108	95	below_threshold
Gemmata obscuriglobus	strain=UQM 2246	GCA_000171775.1	114	114	type	True	76.5921	612	4108	95	below_threshold
Gemmata obscuriglobus	strain=DSM 5831	GCA_003149495.1	114	114	type	True	76.5707	651	4108	95	below_threshold
Gemmata obscuriglobus		GCA_901538385.1	114	114	type	True	76.5533	658	4108	95	below_threshold
Haloferax prahovense	strain=DSM 18310	GCA_000336815.1	381852	381852	type	True	74.682	93	4108	95	below_threshold
Haloferax gibbonsii	strain=ATCC 33959	GCA_000336775.1	35746	35746	type	True	74.6389	122	4108	95	below_threshold
Halomicroarcula limicola	strain=YGHS32	GCA_010119205.1	1429915	1429915	type	True	74.6037	84	4108	95	below_threshold
Haloferax volcanii	strain=DS2	GCA_000337315.1	2246	2246	type	True	74.5654	101	4108	95	below_threshold
Haloferax volcanii	strain=DS2	GCA_000025685.1	2246	2246	type	True	74.5644	102	4108	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:05:21,202] [INFO] DFAST Taxonomy check result was written to GCF_002197845.1_ASM219784v1_genomic.fna/tc_result.tsv
[2024-01-25 20:05:21,203] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:05:21,203] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:05:21,203] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57473330-d6a9-4829-80ec-696a6e37d4ca/dqc_reference/checkm_data
[2024-01-25 20:05:21,204] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:05:21,328] [INFO] Task started: CheckM
[2024-01-25 20:05:21,328] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002197845.1_ASM219784v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002197845.1_ASM219784v1_genomic.fna/checkm_input GCF_002197845.1_ASM219784v1_genomic.fna/checkm_result
[2024-01-25 20:06:50,878] [INFO] Task succeeded: CheckM
[2024-01-25 20:06:50,879] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:06:50,902] [INFO] ===== Completeness check finished =====
[2024-01-25 20:06:50,902] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:06:50,903] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002197845.1_ASM219784v1_genomic.fna/markers.fasta)
[2024-01-25 20:06:50,903] [INFO] Task started: Blastn
[2024-01-25 20:06:50,903] [INFO] Running command: blastn -query GCF_002197845.1_ASM219784v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57473330-d6a9-4829-80ec-696a6e37d4ca/dqc_reference/reference_markers_gtdb.fasta -out GCF_002197845.1_ASM219784v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:06:51,826] [INFO] Task succeeded: Blastn
[2024-01-25 20:06:51,829] [INFO] Selected 14 target genomes.
[2024-01-25 20:06:51,829] [INFO] Target genome list was writen to GCF_002197845.1_ASM219784v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:06:51,863] [INFO] Task started: fastANI
[2024-01-25 20:06:51,863] [INFO] Running command: fastANI --query /var/lib/cwl/stgf289b40b-6b66-46d5-bdf4-29cca0846567/GCF_002197845.1_ASM219784v1_genomic.fna.gz --refList GCF_002197845.1_ASM219784v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002197845.1_ASM219784v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:07:23,394] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:23,404] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:07:23,404] [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_002197845.1	s__Fimbriiglobus ruber	100.0	4097	4108	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Fimbriiglobus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013128195.2	s__Gemmata tundricola	77.0308	748	4108	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008254045.1	s__Limnoglobus roseus	76.9866	750	4108	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Limnoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_901538445.1	s__Gemmata sp901538445	76.9634	795	4108	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822345.1	s__Gemmata sp013822345	76.827	769	4108	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007747215.1	s__Urbifossiella limnaea	76.8048	790	4108	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Urbifossiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308215.1	s__Urbifossiella sp017308215	76.7949	805	4108	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Urbifossiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872595.1	s__Gemmata sp016872595	76.6616	524	4108	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008065095.1	s__Gemmata obscuriglobus	76.622	644	4108	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	99.98	99.95	1.00	1.00	4	-
GCF_901538265.1	s__Gemmata massiliana_A	76.6018	586	4108	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000531095.1	s__Gemmata massiliana	76.5567	551	4108	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	97.81	97.81	0.89	0.89	2	-
GCA_005773755.1	s__Gemmata sp005773755	76.345	352	4108	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005772955.1	s__Gemmata sp005772955	76.1247	328	4108	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	99.91	99.90	0.94	0.93	4	-
GCA_011046615.1	s__DSPQ01 sp011046615	74.6508	75	4108	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__E44-bin32;g__DSPQ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:07:23,405] [INFO] GTDB search result was written to GCF_002197845.1_ASM219784v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:07:23,406] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:07:23,408] [INFO] DFAST_QC result json was written to GCF_002197845.1_ASM219784v1_genomic.fna/dqc_result.json
[2024-01-25 20:07:23,409] [INFO] DFAST_QC completed!
[2024-01-25 20:07:23,409] [INFO] Total running time: 0h3m3s