[2023-06-27 02:41:15,784] [INFO] DFAST_QC pipeline started.
[2023-06-27 02:41:15,786] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 02:41:15,786] [INFO] DQC Reference Directory: /var/lib/cwl/stg6406c52a-0019-478e-a677-573db2441f86/dqc_reference
[2023-06-27 02:41:17,591] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 02:41:17,592] [INFO] Task started: Prodigal
[2023-06-27 02:41:17,593] [INFO] Running command: gunzip -c /var/lib/cwl/stg334b3673-3661-4e46-bc45-61c87673fc63/GCA_026998065.1_ASM2699806v1_genomic.fna.gz | prodigal -d GCA_026998065.1_ASM2699806v1_genomic.fna/cds.fna -a GCA_026998065.1_ASM2699806v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 02:41:28,130] [INFO] Task succeeded: Prodigal
[2023-06-27 02:41:28,131] [INFO] Task started: HMMsearch
[2023-06-27 02:41:28,131] [INFO] Running command: hmmsearch --tblout GCA_026998065.1_ASM2699806v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6406c52a-0019-478e-a677-573db2441f86/dqc_reference/reference_markers.hmm GCA_026998065.1_ASM2699806v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 02:41:28,442] [INFO] Task succeeded: HMMsearch
[2023-06-27 02:41:28,444] [INFO] Found 6/6 markers.
[2023-06-27 02:41:28,575] [INFO] Query marker FASTA was written to GCA_026998065.1_ASM2699806v1_genomic.fna/markers.fasta
[2023-06-27 02:41:28,576] [INFO] Task started: Blastn
[2023-06-27 02:41:28,576] [INFO] Running command: blastn -query GCA_026998065.1_ASM2699806v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6406c52a-0019-478e-a677-573db2441f86/dqc_reference/reference_markers.fasta -out GCA_026998065.1_ASM2699806v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 02:41:29,157] [INFO] Task succeeded: Blastn
[2023-06-27 02:41:29,184] [INFO] Selected 28 target genomes.
[2023-06-27 02:41:29,185] [INFO] Target genome list was writen to GCA_026998065.1_ASM2699806v1_genomic.fna/target_genomes.txt
[2023-06-27 02:41:29,212] [INFO] Task started: fastANI
[2023-06-27 02:41:29,213] [INFO] Running command: fastANI --query /var/lib/cwl/stg334b3673-3661-4e46-bc45-61c87673fc63/GCA_026998065.1_ASM2699806v1_genomic.fna.gz --refList GCA_026998065.1_ASM2699806v1_genomic.fna/target_genomes.txt --output GCA_026998065.1_ASM2699806v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 02:41:45,173] [INFO] Task succeeded: fastANI
[2023-06-27 02:41:45,173] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6406c52a-0019-478e-a677-573db2441f86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 02:41:45,174] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6406c52a-0019-478e-a677-573db2441f86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 02:41:45,182] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 02:41:45,183] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 02:41:45,183] [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
Litorilinea aerophila	strain=ATCC BAA-2444	GCA_006569185.2	1204385	1204385	type	True	75.9245	80	841	95	below_threshold
Streptacidiphilus albus	strain=NBRC 100918	GCA_000787755.1	105425	105425	type	True	74.7312	62	841	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 02:41:45,185] [INFO] DFAST Taxonomy check result was written to GCA_026998065.1_ASM2699806v1_genomic.fna/tc_result.tsv
[2023-06-27 02:41:45,186] [INFO] ===== Taxonomy check completed =====
[2023-06-27 02:41:45,186] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 02:41:45,187] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6406c52a-0019-478e-a677-573db2441f86/dqc_reference/checkm_data
[2023-06-27 02:41:45,188] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 02:41:45,247] [INFO] Task started: CheckM
[2023-06-27 02:41:45,247] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026998065.1_ASM2699806v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026998065.1_ASM2699806v1_genomic.fna/checkm_input GCA_026998065.1_ASM2699806v1_genomic.fna/checkm_result
[2023-06-27 02:42:20,831] [INFO] Task succeeded: CheckM
[2023-06-27 02:42:20,833] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.15%
Contamintation: 8.13%
Strain heterogeneity: 40.00%
--------------------------------------------------------------------------------
[2023-06-27 02:42:20,860] [INFO] ===== Completeness check finished =====
[2023-06-27 02:42:20,861] [INFO] ===== Start GTDB Search =====
[2023-06-27 02:42:20,861] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026998065.1_ASM2699806v1_genomic.fna/markers.fasta)
[2023-06-27 02:42:20,862] [INFO] Task started: Blastn
[2023-06-27 02:42:20,862] [INFO] Running command: blastn -query GCA_026998065.1_ASM2699806v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6406c52a-0019-478e-a677-573db2441f86/dqc_reference/reference_markers_gtdb.fasta -out GCA_026998065.1_ASM2699806v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 02:42:21,674] [INFO] Task succeeded: Blastn
[2023-06-27 02:42:21,697] [INFO] Selected 32 target genomes.
[2023-06-27 02:42:21,698] [INFO] Target genome list was writen to GCA_026998065.1_ASM2699806v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 02:42:21,720] [INFO] Task started: fastANI
[2023-06-27 02:42:21,721] [INFO] Running command: fastANI --query /var/lib/cwl/stg334b3673-3661-4e46-bc45-61c87673fc63/GCA_026998065.1_ASM2699806v1_genomic.fna.gz --refList GCA_026998065.1_ASM2699806v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026998065.1_ASM2699806v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 02:42:38,117] [INFO] Task succeeded: fastANI
[2023-06-27 02:42:38,135] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 02:42:38,135] [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_015484715.1	s__S140-20 sp015484715	99.0002	526	841	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__S140-20;f__S140-20;g__S140-20	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015491235.1	s__WFWG01 sp015491235	76.9914	70	841	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Ardenticatenales;f__Ardenticatenaceae;g__WFWG01	95.0	99.02	98.95	0.84	0.84	3	-
GCA_011192125.1	s__DUEL01 sp011192125	76.9738	138	841	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__B4-G1;f__DUEL01;g__DUEL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015494005.1	s__S144-5 sp015494005	76.872	87	841	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__S144-5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003648085.1	s__B30-G15 sp003648085	76.5098	74	841	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__B4-G1;f__B4-G1;g__B30-G15	95.0	98.10	98.10	0.72	0.72	2	-
GCA_011362935.1	s__SpSt-77 sp011362935	76.5026	100	841	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__B4-G1;f__DUEL01;g__SpSt-77	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014360895.1	s__SpSt-77 sp014360895	76.3604	98	841	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__B4-G1;f__DUEL01;g__SpSt-77	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011334325.1	s__DTPP01 sp011334325	76.0971	87	841	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__DTPP01;f__DTPP01;g__DTPP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011048175.1	s__DSLN01 sp011048175	76.0583	69	841	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__DSLN01;f__DSLN01;g__DSLN01	95.0	99.86	99.86	0.97	0.96	3	-
GCF_006569185.1	s__Litorilinea aerophila	75.9245	80	841	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Litorilinea	95.0	99.85	99.85	0.99	0.99	2	-
GCA_011046405.1	s__DSAR01 sp011046405	75.6967	57	841	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__B4-G1;f__B4-G1;g__DSAR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016783285.1	s__BS750m-G37 sp016783285	75.6615	57	841	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__B4-G1;f__B4-G1;g__BS750m-G37	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017999235.1	s__SpSt-583 sp017999235	75.6464	51	841	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA6663;g__SpSt-583	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011192155.1	s__B4-G1 sp003648025	75.4246	51	841	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__B4-G1;f__B4-G1;g__B4-G1	95.0	99.00	98.99	0.73	0.71	3	-
--------------------------------------------------------------------------------
[2023-06-27 02:42:38,138] [INFO] GTDB search result was written to GCA_026998065.1_ASM2699806v1_genomic.fna/result_gtdb.tsv
[2023-06-27 02:42:38,139] [INFO] ===== GTDB Search completed =====
[2023-06-27 02:42:38,143] [INFO] DFAST_QC result json was written to GCA_026998065.1_ASM2699806v1_genomic.fna/dqc_result.json
[2023-06-27 02:42:38,143] [INFO] DFAST_QC completed!
[2023-06-27 02:42:38,143] [INFO] Total running time: 0h1m22s