[2024-01-25 19:09:20,533] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:09:20,535] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:09:20,535] [INFO] DQC Reference Directory: /var/lib/cwl/stg60ae08d7-d631-40a2-81f5-757922396449/dqc_reference
[2024-01-25 19:09:21,646] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:09:21,646] [INFO] Task started: Prodigal
[2024-01-25 19:09:21,647] [INFO] Running command: gunzip -c /var/lib/cwl/stg81fefff1-c283-4276-b9a4-fe10ee28bcf2/GCF_003173355.1_ASM317335v1_genomic.fna.gz | prodigal -d GCF_003173355.1_ASM317335v1_genomic.fna/cds.fna -a GCF_003173355.1_ASM317335v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:09:29,347] [INFO] Task succeeded: Prodigal
[2024-01-25 19:09:29,347] [INFO] Task started: HMMsearch
[2024-01-25 19:09:29,347] [INFO] Running command: hmmsearch --tblout GCF_003173355.1_ASM317335v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60ae08d7-d631-40a2-81f5-757922396449/dqc_reference/reference_markers.hmm GCF_003173355.1_ASM317335v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:09:29,576] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:09:29,577] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg81fefff1-c283-4276-b9a4-fe10ee28bcf2/GCF_003173355.1_ASM317335v1_genomic.fna.gz]
[2024-01-25 19:09:29,607] [INFO] Query marker FASTA was written to GCF_003173355.1_ASM317335v1_genomic.fna/markers.fasta
[2024-01-25 19:09:29,607] [INFO] Task started: Blastn
[2024-01-25 19:09:29,607] [INFO] Running command: blastn -query GCF_003173355.1_ASM317335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60ae08d7-d631-40a2-81f5-757922396449/dqc_reference/reference_markers.fasta -out GCF_003173355.1_ASM317335v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:09:30,059] [INFO] Task succeeded: Blastn
[2024-01-25 19:09:30,062] [INFO] Selected 8 target genomes.
[2024-01-25 19:09:30,062] [INFO] Target genome list was writen to GCF_003173355.1_ASM317335v1_genomic.fna/target_genomes.txt
[2024-01-25 19:09:30,072] [INFO] Task started: fastANI
[2024-01-25 19:09:30,072] [INFO] Running command: fastANI --query /var/lib/cwl/stg81fefff1-c283-4276-b9a4-fe10ee28bcf2/GCF_003173355.1_ASM317335v1_genomic.fna.gz --refList GCF_003173355.1_ASM317335v1_genomic.fna/target_genomes.txt --output GCF_003173355.1_ASM317335v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:09:35,466] [INFO] Task succeeded: fastANI
[2024-01-25 19:09:35,467] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60ae08d7-d631-40a2-81f5-757922396449/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:09:35,467] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60ae08d7-d631-40a2-81f5-757922396449/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:09:35,472] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:09:35,472] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:09:35,472] [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
Methanospirillum lacunae	strain=Ki8-1	GCA_003173355.1	668570	668570	type	True	100.0	1232	1233	95	conclusive
Methanospirillum hungatei	strain=JF-1	GCA_000013445.1	2203	2203	type	True	77.2956	95	1233	95	below_threshold
Methanospirillum stamsii	strain=Pt1	GCA_003173335.1	1277351	1277351	type	True	76.9723	108	1233	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:09:35,474] [INFO] DFAST Taxonomy check result was written to GCF_003173355.1_ASM317335v1_genomic.fna/tc_result.tsv
[2024-01-25 19:09:35,474] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:09:35,475] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:09:35,475] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60ae08d7-d631-40a2-81f5-757922396449/dqc_reference/checkm_data
[2024-01-25 19:09:35,476] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:09:35,516] [INFO] Task started: CheckM
[2024-01-25 19:09:35,516] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003173355.1_ASM317335v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003173355.1_ASM317335v1_genomic.fna/checkm_input GCF_003173355.1_ASM317335v1_genomic.fna/checkm_result
[2024-01-25 19:10:03,348] [INFO] Task succeeded: CheckM
[2024-01-25 19:10:03,349] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:10:03,377] [INFO] ===== Completeness check finished =====
[2024-01-25 19:10:03,377] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:10:03,377] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003173355.1_ASM317335v1_genomic.fna/markers.fasta)
[2024-01-25 19:10:03,378] [INFO] Task started: Blastn
[2024-01-25 19:10:03,378] [INFO] Running command: blastn -query GCF_003173355.1_ASM317335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60ae08d7-d631-40a2-81f5-757922396449/dqc_reference/reference_markers_gtdb.fasta -out GCF_003173355.1_ASM317335v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:03,865] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:03,867] [INFO] Selected 10 target genomes.
[2024-01-25 19:10:03,867] [INFO] Target genome list was writen to GCF_003173355.1_ASM317335v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:10:03,880] [INFO] Task started: fastANI
[2024-01-25 19:10:03,881] [INFO] Running command: fastANI --query /var/lib/cwl/stg81fefff1-c283-4276-b9a4-fe10ee28bcf2/GCF_003173355.1_ASM317335v1_genomic.fna.gz --refList GCF_003173355.1_ASM317335v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003173355.1_ASM317335v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:10:09,289] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:09,294] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:10:09,294] [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_003173355.1	s__Methanospirillum lacunae	100.0	1232	1233	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanospirillaceae;g__Methanospirillum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003251955.1	s__Methanospirillum hungatei_A	81.4357	276	1233	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanospirillaceae;g__Methanospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019263745.1	s__Methanospirillum sp012729995	77.4112	96	1233	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanospirillaceae;g__Methanospirillum	95.0	98.26	98.06	0.90	0.87	3	-
GCF_000013445.1	s__Methanospirillum hungatei	77.3266	94	1233	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanospirillaceae;g__Methanospirillum	95.0	97.54	96.68	0.94	0.86	5	-
GCF_003173335.1	s__Methanospirillum stamsii	76.952	109	1233	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanospirillaceae;g__Methanospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012729535.1	s__Methanospirillum sp012729535	76.6748	89	1233	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanospirillaceae;g__Methanospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012520015.1	s__Methanospirillum sp012520015	76.6042	55	1233	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanospirillaceae;g__Methanospirillum	95.0	95.42	95.38	0.75	0.70	4	-
--------------------------------------------------------------------------------
[2024-01-25 19:10:09,296] [INFO] GTDB search result was written to GCF_003173355.1_ASM317335v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:10:09,296] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:10:09,298] [INFO] DFAST_QC result json was written to GCF_003173355.1_ASM317335v1_genomic.fna/dqc_result.json
[2024-01-25 19:10:09,298] [INFO] DFAST_QC completed!
[2024-01-25 19:10:09,298] [INFO] Total running time: 0h0m49s