[2023-06-28 13:07:33,132] [INFO] DFAST_QC pipeline started.
[2023-06-28 13:07:33,135] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 13:07:33,135] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3da6381-d28b-4345-a9e1-c391b2d50953/dqc_reference
[2023-06-28 13:07:34,390] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 13:07:34,392] [INFO] Task started: Prodigal
[2023-06-28 13:07:34,392] [INFO] Running command: gunzip -c /var/lib/cwl/stg7a5474b4-bd8b-41c2-8b39-77b5ee044ae0/GCA_002708385.1_ASM270838v1_genomic.fna.gz | prodigal -d GCA_002708385.1_ASM270838v1_genomic.fna/cds.fna -a GCA_002708385.1_ASM270838v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 13:07:36,790] [INFO] Task succeeded: Prodigal
[2023-06-28 13:07:36,791] [INFO] Task started: HMMsearch
[2023-06-28 13:07:36,791] [INFO] Running command: hmmsearch --tblout GCA_002708385.1_ASM270838v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3da6381-d28b-4345-a9e1-c391b2d50953/dqc_reference/reference_markers.hmm GCA_002708385.1_ASM270838v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 13:07:36,946] [INFO] Task succeeded: HMMsearch
[2023-06-28 13:07:36,947] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg7a5474b4-bd8b-41c2-8b39-77b5ee044ae0/GCA_002708385.1_ASM270838v1_genomic.fna.gz]
[2023-06-28 13:07:36,965] [INFO] Query marker FASTA was written to GCA_002708385.1_ASM270838v1_genomic.fna/markers.fasta
[2023-06-28 13:07:36,966] [INFO] Task started: Blastn
[2023-06-28 13:07:36,966] [INFO] Running command: blastn -query GCA_002708385.1_ASM270838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3da6381-d28b-4345-a9e1-c391b2d50953/dqc_reference/reference_markers.fasta -out GCA_002708385.1_ASM270838v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:07:37,417] [INFO] Task succeeded: Blastn
[2023-06-28 13:07:37,421] [INFO] Selected 0 target genomes.
[2023-06-28 13:07:37,421] [INFO] Target genome list was writen to GCA_002708385.1_ASM270838v1_genomic.fna/target_genomes.txt
[2023-06-28 13:07:37,421] [ERROR] File is empty. [GCA_002708385.1_ASM270838v1_genomic.fna/target_genomes.txt]
[2023-06-28 13:07:37,421] [ERROR] Task failed. No target genome found.
[2023-06-28 13:07:37,422] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 13:07:37,422] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3da6381-d28b-4345-a9e1-c391b2d50953/dqc_reference/checkm_data
[2023-06-28 13:07:37,424] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 13:07:37,441] [INFO] Task started: CheckM
[2023-06-28 13:07:37,441] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002708385.1_ASM270838v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002708385.1_ASM270838v1_genomic.fna/checkm_input GCA_002708385.1_ASM270838v1_genomic.fna/checkm_result
[2023-06-28 13:07:52,043] [INFO] Task succeeded: CheckM
[2023-06-28 13:07:52,044] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 13:07:52,076] [INFO] ===== Completeness check finished =====
[2023-06-28 13:07:52,077] [INFO] ===== Start GTDB Search =====
[2023-06-28 13:07:52,077] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002708385.1_ASM270838v1_genomic.fna/markers.fasta)
[2023-06-28 13:07:52,077] [INFO] Task started: Blastn
[2023-06-28 13:07:52,078] [INFO] Running command: blastn -query GCA_002708385.1_ASM270838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3da6381-d28b-4345-a9e1-c391b2d50953/dqc_reference/reference_markers_gtdb.fasta -out GCA_002708385.1_ASM270838v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:07:52,507] [INFO] Task succeeded: Blastn
[2023-06-28 13:07:52,511] [INFO] Selected 9 target genomes.
[2023-06-28 13:07:52,512] [INFO] Target genome list was writen to GCA_002708385.1_ASM270838v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 13:07:52,515] [INFO] Task started: fastANI
[2023-06-28 13:07:52,515] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a5474b4-bd8b-41c2-8b39-77b5ee044ae0/GCA_002708385.1_ASM270838v1_genomic.fna.gz --refList GCA_002708385.1_ASM270838v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002708385.1_ASM270838v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 13:07:54,742] [INFO] Task succeeded: fastANI
[2023-06-28 13:07:54,749] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 13:07:54,750] [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
GCA_002708385.1	s__MGIIb-O1 sp002708385	100.0	356	357	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002502365.1	s__MGIIb-O1 sp002502365	92.0693	243	357	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	96.24	96.24	0.82	0.82	2	-
GCA_002502175.1	s__MGIIb-O1 sp002502175	82.7369	180	357	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	98.79	95.28	0.87	0.80	11	-
GCA_002497025.1	s__MGIIb-O1 sp002497025	81.3299	171	357	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	96.97	96.74	0.84	0.76	4	-
GCA_002685415.1	s__MGIIb-O1 sp002685415	81.074	158	357	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	96.63	96.41	0.81	0.77	3	-
GCA_002457555.1	s__MGIIb-O1 sp002457555	80.5598	179	357	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	99.79	99.79	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-06-28 13:07:54,752] [INFO] GTDB search result was written to GCA_002708385.1_ASM270838v1_genomic.fna/result_gtdb.tsv
[2023-06-28 13:07:54,752] [INFO] ===== GTDB Search completed =====
[2023-06-28 13:07:54,756] [INFO] DFAST_QC result json was written to GCA_002708385.1_ASM270838v1_genomic.fna/dqc_result.json
[2023-06-28 13:07:54,756] [INFO] DFAST_QC completed!
[2023-06-28 13:07:54,756] [INFO] Total running time: 0h0m22s