[2023-06-28 16:01:41,779] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:01:41,781] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:01:41,781] [INFO] DQC Reference Directory: /var/lib/cwl/stg474df94c-cbc4-4cd0-9c13-2d799646417f/dqc_reference
[2023-06-28 16:01:43,032] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:01:43,032] [INFO] Task started: Prodigal
[2023-06-28 16:01:43,033] [INFO] Running command: gunzip -c /var/lib/cwl/stgb8cfb0db-432b-4cb7-972c-1811d73d7397/GCA_019636615.1_ASM1963661v1_genomic.fna.gz | prodigal -d GCA_019636615.1_ASM1963661v1_genomic.fna/cds.fna -a GCA_019636615.1_ASM1963661v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:01:56,469] [INFO] Task succeeded: Prodigal
[2023-06-28 16:01:56,470] [INFO] Task started: HMMsearch
[2023-06-28 16:01:56,470] [INFO] Running command: hmmsearch --tblout GCA_019636615.1_ASM1963661v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg474df94c-cbc4-4cd0-9c13-2d799646417f/dqc_reference/reference_markers.hmm GCA_019636615.1_ASM1963661v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:01:56,683] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:01:56,684] [INFO] Found 6/6 markers.
[2023-06-28 16:01:56,714] [INFO] Query marker FASTA was written to GCA_019636615.1_ASM1963661v1_genomic.fna/markers.fasta
[2023-06-28 16:01:56,714] [INFO] Task started: Blastn
[2023-06-28 16:01:56,714] [INFO] Running command: blastn -query GCA_019636615.1_ASM1963661v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg474df94c-cbc4-4cd0-9c13-2d799646417f/dqc_reference/reference_markers.fasta -out GCA_019636615.1_ASM1963661v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:01:57,341] [INFO] Task succeeded: Blastn
[2023-06-28 16:01:57,345] [INFO] Selected 25 target genomes.
[2023-06-28 16:01:57,345] [INFO] Target genome list was writen to GCA_019636615.1_ASM1963661v1_genomic.fna/target_genomes.txt
[2023-06-28 16:01:57,346] [INFO] Task started: fastANI
[2023-06-28 16:01:57,346] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8cfb0db-432b-4cb7-972c-1811d73d7397/GCA_019636615.1_ASM1963661v1_genomic.fna.gz --refList GCA_019636615.1_ASM1963661v1_genomic.fna/target_genomes.txt --output GCA_019636615.1_ASM1963661v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:02:18,631] [INFO] Task succeeded: fastANI
[2023-06-28 16:02:18,632] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg474df94c-cbc4-4cd0-9c13-2d799646417f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:02:18,632] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg474df94c-cbc4-4cd0-9c13-2d799646417f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:02:18,645] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:02:18,645] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 16:02:18,645] [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
Mucisphaera calidilacus	strain=Pan265	GCA_007748075.1	2527982	2527982	type	True	76.2754	57	1280	95	below_threshold
Algisphaera agarilytica	strain=DSM 103725	GCA_014207595.1	1385975	1385975	type	True	76.2141	71	1280	95	below_threshold
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	75.7764	90	1280	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	75.7312	87	1280	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	75.511	61	1280	95	below_threshold
Humisphaera borealis	strain=M1803	GCA_015169395.1	2807512	2807512	type	True	75.2402	67	1280	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	75.2263	83	1280	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	75.1648	88	1280	95	below_threshold
Paludisphaera borealis	strain=PX4	GCA_001956985.1	1387353	1387353	type	True	75.1277	64	1280	95	below_threshold
Brachybacterium aquaticum	strain=DSM 28796	GCA_014204755.1	1432564	1432564	type	True	74.9789	50	1280	95	below_threshold
Streptomyces pilosus	strain=JCM 4403	GCA_014649835.1	28893	28893	type	True	74.9436	82	1280	95	below_threshold
Brachybacterium saurashtrense	strain=DSM 23186	GCA_003355475.1	556288	556288	type	True	74.8167	52	1280	95	below_threshold
Streptomyces kebangsaanensis	strain=SUK12	GCA_001906585.1	864058	864058	type	True	74.7511	62	1280	95	below_threshold
Streptomyces violaceochromogenes	strain=JCM 4530	GCA_014650235.1	67377	67377	type	True	74.7281	89	1280	95	below_threshold
Dactylosporangium sucinum	strain=JCM 19831	GCA_014647515.1	1424081	1424081	type	True	74.6846	137	1280	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	74.6812	79	1280	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 16:02:18,647] [INFO] DFAST Taxonomy check result was written to GCA_019636615.1_ASM1963661v1_genomic.fna/tc_result.tsv
[2023-06-28 16:02:18,648] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:02:18,648] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:02:18,648] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg474df94c-cbc4-4cd0-9c13-2d799646417f/dqc_reference/checkm_data
[2023-06-28 16:02:18,649] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:02:18,685] [INFO] Task started: CheckM
[2023-06-28 16:02:18,685] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019636615.1_ASM1963661v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019636615.1_ASM1963661v1_genomic.fna/checkm_input GCA_019636615.1_ASM1963661v1_genomic.fna/checkm_result
[2023-06-28 16:03:15,196] [INFO] Task succeeded: CheckM
[2023-06-28 16:03:15,197] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 16:03:15,216] [INFO] ===== Completeness check finished =====
[2023-06-28 16:03:15,217] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:03:15,217] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019636615.1_ASM1963661v1_genomic.fna/markers.fasta)
[2023-06-28 16:03:15,217] [INFO] Task started: Blastn
[2023-06-28 16:03:15,217] [INFO] Running command: blastn -query GCA_019636615.1_ASM1963661v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg474df94c-cbc4-4cd0-9c13-2d799646417f/dqc_reference/reference_markers_gtdb.fasta -out GCA_019636615.1_ASM1963661v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:03:16,057] [INFO] Task succeeded: Blastn
[2023-06-28 16:03:16,061] [INFO] Selected 20 target genomes.
[2023-06-28 16:03:16,061] [INFO] Target genome list was writen to GCA_019636615.1_ASM1963661v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:03:16,064] [INFO] Task started: fastANI
[2023-06-28 16:03:16,064] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8cfb0db-432b-4cb7-972c-1811d73d7397/GCA_019636615.1_ASM1963661v1_genomic.fna.gz --refList GCA_019636615.1_ASM1963661v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019636615.1_ASM1963661v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:03:27,928] [INFO] Task succeeded: fastANI
[2023-06-28 16:03:27,943] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 16:03:27,943] [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_015200025.1	s__UBA2396 sp015200025	79.5639	209	1280	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA2396	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016741915.1	s__JACVCS01 sp016741915	78.9903	158	1280	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JACVCS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303555.1	s__JAFEBO01 sp017303555	78.2291	165	1280	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JAFEBO01	95.0	97.42	97.42	0.91	0.91	2	-
GCA_018242645.1	s__JAFEBO01 sp018242645	78.0212	153	1280	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JAFEBO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013360695.1	s__JABWBC01 sp013360695	77.9347	212	1280	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JABWBC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905339235.1	s__RI-211 sp905339235	77.8449	234	1280	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__RI-211	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002343715.1	s__UBA2402 sp002343715	77.7538	287	1280	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA2402	95.0	96.81	96.81	0.82	0.82	2	-
GCA_903929885.1	s__UBA2402 sp903929885	77.7169	303	1280	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA2402	95.0	99.77	99.77	0.95	0.95	2	-
GCA_018242605.1	s__UBA2402 sp018242605	77.566	323	1280	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA2402	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242625.1	s__JAFEBO01 sp018242625	77.5453	168	1280	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JAFEBO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124375.1	s__RI-211 sp016124375	77.4133	198	1280	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__RI-211	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873295.1	s__VGXM01 sp016873295	77.2037	196	1280	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__VGXM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793195.1	s__JABWBC01 sp016793195	77.065	188	1280	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JABWBC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794925.1	s__JAEUIW01 sp016794925	77.0555	151	1280	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JAEUIW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014584315.1	s__CAADGN01 sp014584315	76.9776	186	1280	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__CAADGN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013285505.1	s__PNC22 sp013285505	76.8837	162	1280	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__PNC22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693765.1	s__RECZ01 sp007693765	76.5005	147	1280	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__RECZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007124345.1	s__SLFH01 sp007124345	76.3101	109	1280	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__SLFH01	95.0	98.92	98.92	0.84	0.84	2	-
GCA_007694925.1	s__SLFH01 sp007694925	76.1995	139	1280	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__SLFH01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 16:03:27,945] [INFO] GTDB search result was written to GCA_019636615.1_ASM1963661v1_genomic.fna/result_gtdb.tsv
[2023-06-28 16:03:27,946] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:03:27,950] [INFO] DFAST_QC result json was written to GCA_019636615.1_ASM1963661v1_genomic.fna/dqc_result.json
[2023-06-28 16:03:27,950] [INFO] DFAST_QC completed!
[2023-06-28 16:03:27,950] [INFO] Total running time: 0h1m46s