[2023-06-27 01:01:24,938] [INFO] DFAST_QC pipeline started.
[2023-06-27 01:01:24,940] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 01:01:24,940] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1150554-692d-45cb-aad2-04f5e4213874/dqc_reference
[2023-06-27 01:01:26,283] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 01:01:26,284] [INFO] Task started: Prodigal
[2023-06-27 01:01:26,285] [INFO] Running command: gunzip -c /var/lib/cwl/stg651d7e27-db69-4728-a9f1-27e4e55e52d9/GCA_026708325.1_ASM2670832v1_genomic.fna.gz | prodigal -d GCA_026708325.1_ASM2670832v1_genomic.fna/cds.fna -a GCA_026708325.1_ASM2670832v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 01:01:36,333] [INFO] Task succeeded: Prodigal
[2023-06-27 01:01:36,333] [INFO] Task started: HMMsearch
[2023-06-27 01:01:36,333] [INFO] Running command: hmmsearch --tblout GCA_026708325.1_ASM2670832v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1150554-692d-45cb-aad2-04f5e4213874/dqc_reference/reference_markers.hmm GCA_026708325.1_ASM2670832v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 01:01:36,622] [INFO] Task succeeded: HMMsearch
[2023-06-27 01:01:36,624] [INFO] Found 6/6 markers.
[2023-06-27 01:01:36,656] [INFO] Query marker FASTA was written to GCA_026708325.1_ASM2670832v1_genomic.fna/markers.fasta
[2023-06-27 01:01:36,656] [INFO] Task started: Blastn
[2023-06-27 01:01:36,657] [INFO] Running command: blastn -query GCA_026708325.1_ASM2670832v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1150554-692d-45cb-aad2-04f5e4213874/dqc_reference/reference_markers.fasta -out GCA_026708325.1_ASM2670832v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 01:01:37,327] [INFO] Task succeeded: Blastn
[2023-06-27 01:01:37,331] [INFO] Selected 29 target genomes.
[2023-06-27 01:01:37,332] [INFO] Target genome list was writen to GCA_026708325.1_ASM2670832v1_genomic.fna/target_genomes.txt
[2023-06-27 01:01:37,340] [INFO] Task started: fastANI
[2023-06-27 01:01:37,340] [INFO] Running command: fastANI --query /var/lib/cwl/stg651d7e27-db69-4728-a9f1-27e4e55e52d9/GCA_026708325.1_ASM2670832v1_genomic.fna.gz --refList GCA_026708325.1_ASM2670832v1_genomic.fna/target_genomes.txt --output GCA_026708325.1_ASM2670832v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 01:01:56,157] [INFO] Task succeeded: fastANI
[2023-06-27 01:01:56,158] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1150554-692d-45cb-aad2-04f5e4213874/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 01:01:56,158] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1150554-692d-45cb-aad2-04f5e4213874/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 01:01:56,176] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 01:01:56,176] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 01:01:56,176] [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
Aggregatilinea lenta	strain=MO-CFX2	GCA_003569045.1	913108	913108	type	True	75.2442	75	1087	95	below_threshold
Streptacidiphilus carbonis	strain=NBRC 100919	GCA_000787775.1	105422	105422	type	True	74.7599	64	1087	95	below_threshold
Streptomyces echinoruber	strain=JCM 5016	GCA_014651135.1	68898	68898	type	True	74.7473	66	1087	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	74.7207	71	1087	95	below_threshold
Streptomyces griseocarneus	strain=CGMCC4.1088	GCA_020093395.1	51201	51201	type	True	74.7055	59	1087	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	74.6893	66	1087	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	74.6789	77	1087	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 01:01:56,179] [INFO] DFAST Taxonomy check result was written to GCA_026708325.1_ASM2670832v1_genomic.fna/tc_result.tsv
[2023-06-27 01:01:56,180] [INFO] ===== Taxonomy check completed =====
[2023-06-27 01:01:56,180] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 01:01:56,180] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1150554-692d-45cb-aad2-04f5e4213874/dqc_reference/checkm_data
[2023-06-27 01:01:56,181] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 01:01:56,219] [INFO] Task started: CheckM
[2023-06-27 01:01:56,219] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026708325.1_ASM2670832v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026708325.1_ASM2670832v1_genomic.fna/checkm_input GCA_026708325.1_ASM2670832v1_genomic.fna/checkm_result
[2023-06-27 01:02:29,113] [INFO] Task succeeded: CheckM
[2023-06-27 01:02:29,115] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 01:02:29,137] [INFO] ===== Completeness check finished =====
[2023-06-27 01:02:29,137] [INFO] ===== Start GTDB Search =====
[2023-06-27 01:02:29,137] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026708325.1_ASM2670832v1_genomic.fna/markers.fasta)
[2023-06-27 01:02:29,138] [INFO] Task started: Blastn
[2023-06-27 01:02:29,138] [INFO] Running command: blastn -query GCA_026708325.1_ASM2670832v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1150554-692d-45cb-aad2-04f5e4213874/dqc_reference/reference_markers_gtdb.fasta -out GCA_026708325.1_ASM2670832v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 01:02:30,092] [INFO] Task succeeded: Blastn
[2023-06-27 01:02:30,097] [INFO] Selected 31 target genomes.
[2023-06-27 01:02:30,097] [INFO] Target genome list was writen to GCA_026708325.1_ASM2670832v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 01:02:30,127] [INFO] Task started: fastANI
[2023-06-27 01:02:30,128] [INFO] Running command: fastANI --query /var/lib/cwl/stg651d7e27-db69-4728-a9f1-27e4e55e52d9/GCA_026708325.1_ASM2670832v1_genomic.fna.gz --refList GCA_026708325.1_ASM2670832v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026708325.1_ASM2670832v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 01:02:51,408] [INFO] Task succeeded: fastANI
[2023-06-27 01:02:51,420] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 01:02:51,420] [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_016788435.1	s__OLB15 sp016788435	76.1387	70	1087	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__OLB15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002238485.1	s__UBA6055 sp002238485	75.926	71	1087	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__UBA6055	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016223085.1	s__CFX2 sp016223085	75.8925	79	1087	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__CFX2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002702065.1	s__GCA-2702065 sp002702065	75.8139	114	1087	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__GCA-2702065	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242205.1	s__ZC4RG36 sp003242205	75.7631	73	1087	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__ZC4RG36	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713325.1	s__OLB15 sp016713325	75.7153	96	1087	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__OLB15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013388735.1	s__CFX2 sp013388735	75.6747	73	1087	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__CFX2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001567485.1	s__OLB13 sp001567485	75.5803	53	1087	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__OLB13	95.0	99.21	98.90	0.94	0.92	9	-
GCA_018432315.1	s__LM3-B42 sp018432315	75.4216	83	1087	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__Aggregatilineaceae;g__LM3-B42	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879765.1	s__JAAEKA01 sp014879765	75.3841	57	1087	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__JAAEKA01;f__JAAEKA01;g__JAAEKA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018056405.1	s__UBA2029 sp018056405	75.3707	50	1087	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__Aggregatilineaceae;g__UBA2029	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003569045.1	s__Aggregatilinea lenta	75.2325	76	1087	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__Aggregatilineaceae;g__Aggregatilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016927535.1	s__JAFGMM01 sp016927535	75.0996	60	1087	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__JAFGMM01;g__JAFGMM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017999235.1	s__SpSt-583 sp017999235	75.0057	65	1087	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA6663;g__SpSt-583	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 01:02:51,422] [INFO] GTDB search result was written to GCA_026708325.1_ASM2670832v1_genomic.fna/result_gtdb.tsv
[2023-06-27 01:02:51,423] [INFO] ===== GTDB Search completed =====
[2023-06-27 01:02:51,426] [INFO] DFAST_QC result json was written to GCA_026708325.1_ASM2670832v1_genomic.fna/dqc_result.json
[2023-06-27 01:02:51,426] [INFO] DFAST_QC completed!
[2023-06-27 01:02:51,426] [INFO] Total running time: 0h1m26s