[2023-06-30 00:25:28,237] [INFO] DFAST_QC pipeline started.
[2023-06-30 00:25:28,239] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 00:25:28,239] [INFO] DQC Reference Directory: /var/lib/cwl/stgbff8bbeb-645b-415f-ba0d-c32aebb70e0c/dqc_reference
[2023-06-30 00:25:29,412] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 00:25:29,413] [INFO] Task started: Prodigal
[2023-06-30 00:25:29,413] [INFO] Running command: gunzip -c /var/lib/cwl/stg93e47aab-8946-4fe4-b7ad-da89084a1994/GCA_903898975.1_freshwater_MAG_---_LaPlata-a_bin-1986_genomic.fna.gz | prodigal -d GCA_903898975.1_freshwater_MAG_---_LaPlata-a_bin-1986_genomic.fna/cds.fna -a GCA_903898975.1_freshwater_MAG_---_LaPlata-a_bin-1986_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 00:25:44,553] [INFO] Task succeeded: Prodigal
[2023-06-30 00:25:44,553] [INFO] Task started: HMMsearch
[2023-06-30 00:25:44,553] [INFO] Running command: hmmsearch --tblout GCA_903898975.1_freshwater_MAG_---_LaPlata-a_bin-1986_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbff8bbeb-645b-415f-ba0d-c32aebb70e0c/dqc_reference/reference_markers.hmm GCA_903898975.1_freshwater_MAG_---_LaPlata-a_bin-1986_genomic.fna/protein.faa > /dev/null
[2023-06-30 00:25:44,862] [INFO] Task succeeded: HMMsearch
[2023-06-30 00:25:44,864] [INFO] Found 6/6 markers.
[2023-06-30 00:25:44,912] [INFO] Query marker FASTA was written to GCA_903898975.1_freshwater_MAG_---_LaPlata-a_bin-1986_genomic.fna/markers.fasta
[2023-06-30 00:25:44,913] [INFO] Task started: Blastn
[2023-06-30 00:25:44,913] [INFO] Running command: blastn -query GCA_903898975.1_freshwater_MAG_---_LaPlata-a_bin-1986_genomic.fna/markers.fasta -db /var/lib/cwl/stgbff8bbeb-645b-415f-ba0d-c32aebb70e0c/dqc_reference/reference_markers.fasta -out GCA_903898975.1_freshwater_MAG_---_LaPlata-a_bin-1986_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:25:45,521] [INFO] Task succeeded: Blastn
[2023-06-30 00:25:45,526] [INFO] Selected 22 target genomes.
[2023-06-30 00:25:45,527] [INFO] Target genome list was writen to GCA_903898975.1_freshwater_MAG_---_LaPlata-a_bin-1986_genomic.fna/target_genomes.txt
[2023-06-30 00:25:45,529] [INFO] Task started: fastANI
[2023-06-30 00:25:45,529] [INFO] Running command: fastANI --query /var/lib/cwl/stg93e47aab-8946-4fe4-b7ad-da89084a1994/GCA_903898975.1_freshwater_MAG_---_LaPlata-a_bin-1986_genomic.fna.gz --refList GCA_903898975.1_freshwater_MAG_---_LaPlata-a_bin-1986_genomic.fna/target_genomes.txt --output GCA_903898975.1_freshwater_MAG_---_LaPlata-a_bin-1986_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 00:26:03,403] [INFO] Task succeeded: fastANI
[2023-06-30 00:26:03,404] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbff8bbeb-645b-415f-ba0d-c32aebb70e0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 00:26:03,404] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbff8bbeb-645b-415f-ba0d-c32aebb70e0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 00:26:03,418] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 00:26:03,418] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 00:26:03,418] [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
Caulifigura coniformis	strain=Pan44	GCA_007745175.1	2527983	2527983	type	True	75.4035	63	1260	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	75.1898	58	1260	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	75.1351	79	1260	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	74.9893	83	1260	95	below_threshold
Alienimonas chondri	strain=LzC2	GCA_013036045.1	2681879	2681879	type	True	74.7712	51	1260	95	below_threshold
Catellatospora citrea	strain=NBRC 14495	GCA_016862615.1	53366	53366	type	True	74.6474	66	1260	95	below_threshold
Geodermatophilus bullaregiensis	strain=DSM 46841	GCA_016907675.1	1564160	1564160	type	True	74.5707	56	1260	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 00:26:03,420] [INFO] DFAST Taxonomy check result was written to GCA_903898975.1_freshwater_MAG_---_LaPlata-a_bin-1986_genomic.fna/tc_result.tsv
[2023-06-30 00:26:03,421] [INFO] ===== Taxonomy check completed =====
[2023-06-30 00:26:03,421] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 00:26:03,421] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbff8bbeb-645b-415f-ba0d-c32aebb70e0c/dqc_reference/checkm_data
[2023-06-30 00:26:03,422] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 00:26:03,484] [INFO] Task started: CheckM
[2023-06-30 00:26:03,484] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903898975.1_freshwater_MAG_---_LaPlata-a_bin-1986_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903898975.1_freshwater_MAG_---_LaPlata-a_bin-1986_genomic.fna/checkm_input GCA_903898975.1_freshwater_MAG_---_LaPlata-a_bin-1986_genomic.fna/checkm_result
[2023-06-30 00:26:52,074] [INFO] Task succeeded: CheckM
[2023-06-30 00:26:52,075] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.08%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 00:26:52,107] [INFO] ===== Completeness check finished =====
[2023-06-30 00:26:52,107] [INFO] ===== Start GTDB Search =====
[2023-06-30 00:26:52,108] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903898975.1_freshwater_MAG_---_LaPlata-a_bin-1986_genomic.fna/markers.fasta)
[2023-06-30 00:26:52,108] [INFO] Task started: Blastn
[2023-06-30 00:26:52,108] [INFO] Running command: blastn -query GCA_903898975.1_freshwater_MAG_---_LaPlata-a_bin-1986_genomic.fna/markers.fasta -db /var/lib/cwl/stgbff8bbeb-645b-415f-ba0d-c32aebb70e0c/dqc_reference/reference_markers_gtdb.fasta -out GCA_903898975.1_freshwater_MAG_---_LaPlata-a_bin-1986_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:26:52,905] [INFO] Task succeeded: Blastn
[2023-06-30 00:26:52,910] [INFO] Selected 29 target genomes.
[2023-06-30 00:26:52,910] [INFO] Target genome list was writen to GCA_903898975.1_freshwater_MAG_---_LaPlata-a_bin-1986_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 00:26:52,921] [INFO] Task started: fastANI
[2023-06-30 00:26:52,921] [INFO] Running command: fastANI --query /var/lib/cwl/stg93e47aab-8946-4fe4-b7ad-da89084a1994/GCA_903898975.1_freshwater_MAG_---_LaPlata-a_bin-1986_genomic.fna.gz --refList GCA_903898975.1_freshwater_MAG_---_LaPlata-a_bin-1986_genomic.fna/target_genomes_gtdb.txt --output GCA_903898975.1_freshwater_MAG_---_LaPlata-a_bin-1986_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 00:27:15,582] [INFO] Task succeeded: fastANI
[2023-06-30 00:27:15,591] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 00:27:15,591] [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_003508595.1	s__UBA10511 sp003508595	79.7573	296	1260	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__UBA10511;g__UBA10511	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903861195.1	s__UBA10511 sp903861195	77.628	290	1260	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__UBA10511;g__UBA10511	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200145.1	s__JACQFH01 sp016200145	75.8072	113	1260	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__UBA10511;g__JACQFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001610835.1	s__Planctomyces_A sp001610835	75.4729	98	1260	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Planctomyces_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822855.1	s__Planctopirus sp013822855	75.3957	52	1260	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Planctopirus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009691905.1	s__SIAF01 sp009691905	75.3129	94	1260	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__UBA10511;g__SIAF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 00:27:15,593] [INFO] GTDB search result was written to GCA_903898975.1_freshwater_MAG_---_LaPlata-a_bin-1986_genomic.fna/result_gtdb.tsv
[2023-06-30 00:27:15,593] [INFO] ===== GTDB Search completed =====
[2023-06-30 00:27:15,606] [INFO] DFAST_QC result json was written to GCA_903898975.1_freshwater_MAG_---_LaPlata-a_bin-1986_genomic.fna/dqc_result.json
[2023-06-30 00:27:15,606] [INFO] DFAST_QC completed!
[2023-06-30 00:27:15,606] [INFO] Total running time: 0h1m47s