[2024-01-24 14:23:01,870] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:23:01,872] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:23:01,872] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2213072-a493-4a16-a59a-f7179a528aa0/dqc_reference
[2024-01-24 14:23:03,111] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:03,112] [INFO] Task started: Prodigal
[2024-01-24 14:23:03,112] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ab1860f-6fa6-4e6b-8549-fe7a804075e6/GCF_007744515.1_ASM774451v1_genomic.fna.gz | prodigal -d GCF_007744515.1_ASM774451v1_genomic.fna/cds.fna -a GCF_007744515.1_ASM774451v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:18,196] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:18,196] [INFO] Task started: HMMsearch
[2024-01-24 14:23:18,196] [INFO] Running command: hmmsearch --tblout GCF_007744515.1_ASM774451v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2213072-a493-4a16-a59a-f7179a528aa0/dqc_reference/reference_markers.hmm GCF_007744515.1_ASM774451v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:18,525] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:18,526] [INFO] Found 6/6 markers.
[2024-01-24 14:23:18,574] [INFO] Query marker FASTA was written to GCF_007744515.1_ASM774451v1_genomic.fna/markers.fasta
[2024-01-24 14:23:18,575] [INFO] Task started: Blastn
[2024-01-24 14:23:18,575] [INFO] Running command: blastn -query GCF_007744515.1_ASM774451v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2213072-a493-4a16-a59a-f7179a528aa0/dqc_reference/reference_markers.fasta -out GCF_007744515.1_ASM774451v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:19,203] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:19,207] [INFO] Selected 28 target genomes.
[2024-01-24 14:23:19,208] [INFO] Target genome list was writen to GCF_007744515.1_ASM774451v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:19,226] [INFO] Task started: fastANI
[2024-01-24 14:23:19,226] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ab1860f-6fa6-4e6b-8549-fe7a804075e6/GCF_007744515.1_ASM774451v1_genomic.fna.gz --refList GCF_007744515.1_ASM774451v1_genomic.fna/target_genomes.txt --output GCF_007744515.1_ASM774451v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:45,161] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:45,162] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2213072-a493-4a16-a59a-f7179a528aa0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:45,162] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2213072-a493-4a16-a59a-f7179a528aa0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:45,172] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:23:45,172] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:23:45,173] [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
Calycomorphotria hydatis	strain=V22	GCA_007745435.1	2528027	2528027	type	True	76.4012	138	1742	95	below_threshold
Alienimonas californiensis	strain=CA12	GCA_007743815.1	2527989	2527989	type	True	76.1834	110	1742	95	below_threshold
Alienimonas chondri	strain=LzC2	GCA_013036045.1	2681879	2681879	type	True	75.9265	104	1742	95	below_threshold
Rubinisphaera brasiliensis	strain=DSM 5305	GCA_000165715.3	119	119	type	True	75.8622	59	1742	95	below_threshold
Lacipirellula parvula	strain=PX69	GCA_009177095.1	2650471	2650471	type	True	75.7169	62	1742	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	75.6665	63	1742	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	75.4997	69	1742	95	below_threshold
Blastopirellula retiformator	strain=Enr8	GCA_007859755.1	2527970	2527970	type	True	75.2814	52	1742	95	below_threshold
Lignipirellula cremea	strain=Pla85_3_4	GCA_007751035.1	2528010	2528010	type	True	75.2701	58	1742	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	75.2074	55	1742	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:45,174] [INFO] DFAST Taxonomy check result was written to GCF_007744515.1_ASM774451v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:45,175] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:45,175] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:45,175] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2213072-a493-4a16-a59a-f7179a528aa0/dqc_reference/checkm_data
[2024-01-24 14:23:45,176] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:45,227] [INFO] Task started: CheckM
[2024-01-24 14:23:45,227] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007744515.1_ASM774451v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007744515.1_ASM774451v1_genomic.fna/checkm_input GCF_007744515.1_ASM774451v1_genomic.fna/checkm_result
[2024-01-24 14:24:30,437] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:30,440] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:30,465] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:30,465] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:30,466] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007744515.1_ASM774451v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:30,466] [INFO] Task started: Blastn
[2024-01-24 14:24:30,466] [INFO] Running command: blastn -query GCF_007744515.1_ASM774451v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2213072-a493-4a16-a59a-f7179a528aa0/dqc_reference/reference_markers_gtdb.fasta -out GCF_007744515.1_ASM774451v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:31,313] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:31,317] [INFO] Selected 29 target genomes.
[2024-01-24 14:24:31,318] [INFO] Target genome list was writen to GCF_007744515.1_ASM774451v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:31,357] [INFO] Task started: fastANI
[2024-01-24 14:24:31,357] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ab1860f-6fa6-4e6b-8549-fe7a804075e6/GCF_007744515.1_ASM774451v1_genomic.fna.gz --refList GCF_007744515.1_ASM774451v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007744515.1_ASM774451v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:55,637] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:55,649] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:55,649] [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_007744515.1	s__Calycomorphotria sp007744515	99.9995	1740	1742	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Calycomorphotria	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007745435.1	s__Calycomorphotria hydatis	76.3631	137	1742	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Calycomorphotria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007743815.1	s__Alienimonas californiensis	76.1834	110	1742	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Alienimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013813775.1	s__JACCRE01 sp013813775	75.9694	132	1742	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JACCRE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013036045.1	s__Alienimonas chondri	75.9265	104	1742	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Alienimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003669125.1	s__SXKJ01 sp003669125	75.6626	56	1742	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXKJ01	95.0	99.07	98.94	0.92	0.91	3	-
GCA_016795125.1	s__JAEUIG01 sp016795125	75.3454	55	1742	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JAEUIG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124895.1	s__JABMPE01 sp016124895	75.2824	75	1742	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABMPE01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:55,651] [INFO] GTDB search result was written to GCF_007744515.1_ASM774451v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:55,651] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:55,654] [INFO] DFAST_QC result json was written to GCF_007744515.1_ASM774451v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:55,655] [INFO] DFAST_QC completed!
[2024-01-24 14:24:55,655] [INFO] Total running time: 0h1m54s