[2023-03-18 10:15:15,039] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:15:15,039] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:15:15,039] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c95a007-2521-4f27-9f0d-5f2cd358c244/dqc_reference
[2023-03-18 10:15:16,171] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:15:16,172] [INFO] Task started: Prodigal
[2023-03-18 10:15:16,172] [INFO] Running command: cat /var/lib/cwl/stgfcb3aa0b-9a50-4075-bed5-145d9276e64c/OceanDNA-b1765.fa | prodigal -d OceanDNA-b1765/cds.fna -a OceanDNA-b1765/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:15:29,385] [INFO] Task succeeded: Prodigal
[2023-03-18 10:15:29,386] [INFO] Task started: HMMsearch
[2023-03-18 10:15:29,386] [INFO] Running command: hmmsearch --tblout OceanDNA-b1765/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c95a007-2521-4f27-9f0d-5f2cd358c244/dqc_reference/reference_markers.hmm OceanDNA-b1765/protein.faa > /dev/null
[2023-03-18 10:15:29,578] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:15:29,579] [INFO] Found 6/6 markers.
[2023-03-18 10:15:29,598] [INFO] Query marker FASTA was written to OceanDNA-b1765/markers.fasta
[2023-03-18 10:15:29,599] [INFO] Task started: Blastn
[2023-03-18 10:15:29,599] [INFO] Running command: blastn -query OceanDNA-b1765/markers.fasta -db /var/lib/cwl/stg3c95a007-2521-4f27-9f0d-5f2cd358c244/dqc_reference/reference_markers.fasta -out OceanDNA-b1765/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:15:30,348] [INFO] Task succeeded: Blastn
[2023-03-18 10:15:30,349] [INFO] Selected 30 target genomes.
[2023-03-18 10:15:30,349] [INFO] Target genome list was writen to OceanDNA-b1765/target_genomes.txt
[2023-03-18 10:15:30,383] [INFO] Task started: fastANI
[2023-03-18 10:15:30,384] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcb3aa0b-9a50-4075-bed5-145d9276e64c/OceanDNA-b1765.fa --refList OceanDNA-b1765/target_genomes.txt --output OceanDNA-b1765/fastani_result.tsv --threads 1
[2023-03-18 10:15:53,131] [INFO] Task succeeded: fastANI
[2023-03-18 10:15:53,132] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c95a007-2521-4f27-9f0d-5f2cd358c244/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:15:53,132] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c95a007-2521-4f27-9f0d-5f2cd358c244/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:15:53,143] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:15:53,143] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 10:15:53,143] [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
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.533	132	700	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.4666	151	700	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.1711	88	700	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.0705	141	700	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	76.0523	103	700	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.6661	139	700	95	below_threshold
Gordonia paraffinivorans	strain=NBRC 108238	GCA_000344155.1	175628	175628	type	True	75.4154	62	700	95	below_threshold
Nocardioides halotolerans	strain=DSM 19273	GCA_000422805.1	433660	433660	type	True	75.2615	56	700	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	75.1806	59	700	95	below_threshold
Micromonospora phaseoli	strain=CGMCC 4.7038	GCA_900109115.1	1144548	1144548	type	True	75.1674	60	700	95	below_threshold
Saccharopolyspora phatthalungensis	strain=DSM 45584	GCA_014203395.1	664693	664693	type	True	75.1609	50	700	95	below_threshold
Micromonospora phaseoli	strain=DSM 45730	GCA_003253475.1	1144548	1144548	type	True	75.1541	61	700	95	below_threshold
Pseudonocardia nigra	strain=DSM 104088	GCA_019396355.1	1921578	1921578	type	True	75.1287	95	700	95	below_threshold
Saccharopolyspora spinosa	strain=NRRL 18395	GCA_000194155.1	60894	60894	type	True	74.9806	51	700	95	below_threshold
Saccharopolyspora spinosa	strain=DSM 44228	GCA_002846475.1	60894	60894	type	True	74.9742	52	700	95	below_threshold
Nocardioides plantarum	strain=DSM 11054	GCA_006346395.1	29299	29299	type	True	74.9619	61	700	95	below_threshold
Saccharopolyspora elongata	strain=7K502	GCA_004348985.1	2530387	2530387	type	True	74.9245	74	700	95	below_threshold
Kineococcus radiotolerans	strain=SRS30216	GCA_000017305.1	131568	131568	type	True	74.7657	52	700	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 10:15:53,144] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1765/tc_result.tsv
[2023-03-18 10:15:53,144] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:15:53,144] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:15:53,144] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c95a007-2521-4f27-9f0d-5f2cd358c244/dqc_reference/checkm_data
[2023-03-18 10:15:53,145] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:15:53,149] [INFO] Task started: CheckM
[2023-03-18 10:15:53,149] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1765/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1765/checkm_input OceanDNA-b1765/checkm_result
[2023-03-18 10:16:38,973] [INFO] Task succeeded: CheckM
[2023-03-18 10:16:38,974] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:16:38,997] [INFO] ===== Completeness check finished =====
[2023-03-18 10:16:38,998] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:16:38,998] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1765/markers.fasta)
[2023-03-18 10:16:38,998] [INFO] Task started: Blastn
[2023-03-18 10:16:38,998] [INFO] Running command: blastn -query OceanDNA-b1765/markers.fasta -db /var/lib/cwl/stg3c95a007-2521-4f27-9f0d-5f2cd358c244/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1765/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:16:40,285] [INFO] Task succeeded: Blastn
[2023-03-18 10:16:40,286] [INFO] Selected 10 target genomes.
[2023-03-18 10:16:40,286] [INFO] Target genome list was writen to OceanDNA-b1765/target_genomes_gtdb.txt
[2023-03-18 10:16:40,314] [INFO] Task started: fastANI
[2023-03-18 10:16:40,314] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcb3aa0b-9a50-4075-bed5-145d9276e64c/OceanDNA-b1765.fa --refList OceanDNA-b1765/target_genomes_gtdb.txt --output OceanDNA-b1765/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:16:46,177] [INFO] Task succeeded: fastANI
[2023-03-18 10:16:46,184] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 10:16:46,184] [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_002694825.1	s__UBA11606 sp002694825	94.082	588	700	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	97.28	96.77	0.84	0.81	7	-
GCA_002699625.1	s__UBA11606 sp002699625	93.5807	512	700	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729125.1	s__UBA11606 sp002729125	91.2704	585	700	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	99.78	99.78	0.92	0.92	2	-
GCA_016845585.1	s__UBA11606 sp016845585	78.6085	296	700	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480195.1	s__UBA11606 sp905480195	78.2399	287	700	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003231645.1	s__SZUA-87 sp003231645	76.9216	144	700	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__SZUA-87	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937405.1	s__UBA11606 sp009937405	76.7959	151	700	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	99.36	99.36	0.86	0.86	2	-
GCA_013002375.1	s__JABDJW01 sp013002375	76.3635	118	700	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SHLQ01;g__JABDJW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185275.1	s__JACPNX01 sp016185275	76.095	101	700	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JACPNX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017577565.1	s__ZC4RG19 sp017577565	75.956	115	700	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:16:46,188] [INFO] GTDB search result was written to OceanDNA-b1765/result_gtdb.tsv
[2023-03-18 10:16:46,191] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:16:46,195] [INFO] DFAST_QC result json was written to OceanDNA-b1765/dqc_result.json
[2023-03-18 10:16:46,195] [INFO] DFAST_QC completed!
[2023-03-18 10:16:46,195] [INFO] Total running time: 0h1m31s