[2023-06-18 19:52:04,673] [INFO] DFAST_QC pipeline started.
[2023-06-18 19:52:04,676] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 19:52:04,676] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f5e4d96-3480-460a-a461-09bbfecb473c/dqc_reference
[2023-06-18 19:52:06,115] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 19:52:06,115] [INFO] Task started: Prodigal
[2023-06-18 19:52:06,116] [INFO] Running command: gunzip -c /var/lib/cwl/stg5db59a96-4d13-4454-ad48-f1aefd99b955/GCA_018335035.1_ASM1833503v1_genomic.fna.gz | prodigal -d GCA_018335035.1_ASM1833503v1_genomic.fna/cds.fna -a GCA_018335035.1_ASM1833503v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 19:52:14,111] [INFO] Task succeeded: Prodigal
[2023-06-18 19:52:14,112] [INFO] Task started: HMMsearch
[2023-06-18 19:52:14,112] [INFO] Running command: hmmsearch --tblout GCA_018335035.1_ASM1833503v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f5e4d96-3480-460a-a461-09bbfecb473c/dqc_reference/reference_markers.hmm GCA_018335035.1_ASM1833503v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 19:52:14,372] [INFO] Task succeeded: HMMsearch
[2023-06-18 19:52:14,378] [INFO] Found 6/6 markers.
[2023-06-18 19:52:14,409] [INFO] Query marker FASTA was written to GCA_018335035.1_ASM1833503v1_genomic.fna/markers.fasta
[2023-06-18 19:52:14,410] [INFO] Task started: Blastn
[2023-06-18 19:52:14,410] [INFO] Running command: blastn -query GCA_018335035.1_ASM1833503v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f5e4d96-3480-460a-a461-09bbfecb473c/dqc_reference/reference_markers.fasta -out GCA_018335035.1_ASM1833503v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 19:52:15,074] [INFO] Task succeeded: Blastn
[2023-06-18 19:52:15,078] [INFO] Selected 29 target genomes.
[2023-06-18 19:52:15,078] [INFO] Target genome list was writen to GCA_018335035.1_ASM1833503v1_genomic.fna/target_genomes.txt
[2023-06-18 19:52:15,084] [INFO] Task started: fastANI
[2023-06-18 19:52:15,084] [INFO] Running command: fastANI --query /var/lib/cwl/stg5db59a96-4d13-4454-ad48-f1aefd99b955/GCA_018335035.1_ASM1833503v1_genomic.fna.gz --refList GCA_018335035.1_ASM1833503v1_genomic.fna/target_genomes.txt --output GCA_018335035.1_ASM1833503v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 19:52:35,074] [INFO] Task succeeded: fastANI
[2023-06-18 19:52:35,074] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f5e4d96-3480-460a-a461-09bbfecb473c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 19:52:35,075] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f5e4d96-3480-460a-a461-09bbfecb473c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 19:52:35,097] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 19:52:35,098] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 19:52:35,098] [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
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	75.6606	81	871	95	below_threshold
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	75.6141	84	871	95	below_threshold
Humisphaera borealis	strain=M1803	GCA_015169395.1	2807512	2807512	type	True	75.4765	67	871	95	below_threshold
Paludisphaera borealis	strain=PX4	GCA_001956985.1	1387353	1387353	type	True	75.4411	81	871	95	below_threshold
Botrimarina mediterranea	strain=Spa11	GCA_007753265.1	2528022	2528022	type	True	75.421	54	871	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	75.3702	94	871	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.1488	89	871	95	below_threshold
Rubrimonas cliftonensis	strain=DSM 15345	GCA_900107585.1	89524	89524	type	True	74.8956	89	871	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	74.8703	50	871	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	74.8337	92	871	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	74.8101	53	871	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	74.7045	69	871	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013409965.1	419476	419476	type	True	74.6999	70	871	95	below_threshold
Glycomyces artemisiae	strain=CGMCC 4.7067	GCA_003002955.1	1076443	1076443	type	True	74.6699	78	871	95	below_threshold
Glycomyces sambucus	strain=CGMCC 4.3147	GCA_900102815.1	380244	380244	type	True	74.6609	67	871	95	below_threshold
Glycomyces terrestris	strain=YIM 121974	GCA_003933745.1	2493553	2493553	type	True	74.6424	81	871	95	below_threshold
Glycomyces dulcitolivorans	strain=SJ-25	GCA_003265355.1	2200759	2200759	type	True	74.6323	73	871	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 19:52:35,100] [INFO] DFAST Taxonomy check result was written to GCA_018335035.1_ASM1833503v1_genomic.fna/tc_result.tsv
[2023-06-18 19:52:35,100] [INFO] ===== Taxonomy check completed =====
[2023-06-18 19:52:35,100] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 19:52:35,101] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f5e4d96-3480-460a-a461-09bbfecb473c/dqc_reference/checkm_data
[2023-06-18 19:52:35,102] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 19:52:35,136] [INFO] Task started: CheckM
[2023-06-18 19:52:35,136] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018335035.1_ASM1833503v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018335035.1_ASM1833503v1_genomic.fna/checkm_input GCA_018335035.1_ASM1833503v1_genomic.fna/checkm_result
[2023-06-18 19:53:02,595] [INFO] Task succeeded: CheckM
[2023-06-18 19:53:02,597] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 19:53:02,626] [INFO] ===== Completeness check finished =====
[2023-06-18 19:53:02,626] [INFO] ===== Start GTDB Search =====
[2023-06-18 19:53:02,627] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018335035.1_ASM1833503v1_genomic.fna/markers.fasta)
[2023-06-18 19:53:02,627] [INFO] Task started: Blastn
[2023-06-18 19:53:02,628] [INFO] Running command: blastn -query GCA_018335035.1_ASM1833503v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f5e4d96-3480-460a-a461-09bbfecb473c/dqc_reference/reference_markers_gtdb.fasta -out GCA_018335035.1_ASM1833503v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 19:53:03,617] [INFO] Task succeeded: Blastn
[2023-06-18 19:53:03,623] [INFO] Selected 19 target genomes.
[2023-06-18 19:53:03,623] [INFO] Target genome list was writen to GCA_018335035.1_ASM1833503v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 19:53:03,633] [INFO] Task started: fastANI
[2023-06-18 19:53:03,633] [INFO] Running command: fastANI --query /var/lib/cwl/stg5db59a96-4d13-4454-ad48-f1aefd99b955/GCA_018335035.1_ASM1833503v1_genomic.fna.gz --refList GCA_018335035.1_ASM1833503v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018335035.1_ASM1833503v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 19:53:16,238] [INFO] Task succeeded: fastANI
[2023-06-18 19:53:16,254] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 19:53:16,255] [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_018335035.1	s__JAGXKT01 sp018335035	100.0	865	871	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__SM23-33;f__SM23-33;g__JAGXKT01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009908915.1	s__JAAAOJ01 sp009908915	77.337	123	871	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__SM23-33;f__SM23-33;g__JAAAOJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003485185.1	s__UBA12270 sp003485185	77.0517	219	871	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__SM23-33;f__SM23-33;g__UBA12270	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002071695.1	s__MWDR01 sp002071695	76.7271	212	871	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__SM23-33;f__SM23-33;g__MWDR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003551645.1	s__PUND01 sp003551645	76.6808	129	871	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__SM23-33;f__SM23-33;g__PUND01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001303665.1	s__SM23-33 sp001303665	76.6711	118	871	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__SM23-33;f__SM23-33;g__SM23-33	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050235.1	s__HyVt-337 sp011050235	76.6147	146	871	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__SM23-33;f__SM23-33;g__HyVt-337	95.0	99.95	99.95	0.96	0.96	2	-
GCA_012729725.1	s__JAAYCO01 sp012729725	76.5046	68	871	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__SM23-33;f__SM23-33;g__JAAYCO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235825.1	s__JACRIL01 sp016235825	76.4109	115	871	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__SM23-33;f__SM23-33;g__JACRIL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873255.1	s__UBA966 sp016873255	76.0855	51	871	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA966	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007119405.1	s__SKPT01 sp007119405	75.6142	54	871	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__SKPT01	95.0	98.45	98.45	0.84	0.84	2	-
GCF_015169395.1	s__Humisphaera borealis	75.4765	67	871	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Tepidisphaerales;f__Tepidisphaeraceae;g__Humisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016699855.1	s__GCA-016699855 sp016699855	75.0355	91	871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__GCA-016699855	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107585.1	s__Rubrimonas cliftonensis	74.8748	94	871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubrimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 19:53:16,257] [INFO] GTDB search result was written to GCA_018335035.1_ASM1833503v1_genomic.fna/result_gtdb.tsv
[2023-06-18 19:53:16,257] [INFO] ===== GTDB Search completed =====
[2023-06-18 19:53:16,261] [INFO] DFAST_QC result json was written to GCA_018335035.1_ASM1833503v1_genomic.fna/dqc_result.json
[2023-06-18 19:53:16,261] [INFO] DFAST_QC completed!
[2023-06-18 19:53:16,261] [INFO] Total running time: 0h1m12s