[2023-03-15 08:09:45,351] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:09:45,352] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:09:45,352] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e594e73-7a21-4aa0-a573-949a060d73ef/dqc_reference
[2023-03-15 08:09:46,748] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:09:46,749] [INFO] Task started: Prodigal
[2023-03-15 08:09:46,749] [INFO] Running command: cat /var/lib/cwl/stg73116b7d-2785-4e3c-b334-83e41633881b/OceanDNA-b23099.fa | prodigal -d OceanDNA-b23099/cds.fna -a OceanDNA-b23099/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:10:10,986] [INFO] Task succeeded: Prodigal
[2023-03-15 08:10:10,986] [INFO] Task started: HMMsearch
[2023-03-15 08:10:10,986] [INFO] Running command: hmmsearch --tblout OceanDNA-b23099/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e594e73-7a21-4aa0-a573-949a060d73ef/dqc_reference/reference_markers.hmm OceanDNA-b23099/protein.faa > /dev/null
[2023-03-15 08:10:11,257] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:10:11,258] [INFO] Found 6/6 markers.
[2023-03-15 08:10:11,285] [INFO] Query marker FASTA was written to OceanDNA-b23099/markers.fasta
[2023-03-15 08:10:11,286] [INFO] Task started: Blastn
[2023-03-15 08:10:11,286] [INFO] Running command: blastn -query OceanDNA-b23099/markers.fasta -db /var/lib/cwl/stg8e594e73-7a21-4aa0-a573-949a060d73ef/dqc_reference/reference_markers.fasta -out OceanDNA-b23099/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:10:12,012] [INFO] Task succeeded: Blastn
[2023-03-15 08:10:12,013] [INFO] Selected 24 target genomes.
[2023-03-15 08:10:12,013] [INFO] Target genome list was writen to OceanDNA-b23099/target_genomes.txt
[2023-03-15 08:10:12,028] [INFO] Task started: fastANI
[2023-03-15 08:10:12,028] [INFO] Running command: fastANI --query /var/lib/cwl/stg73116b7d-2785-4e3c-b334-83e41633881b/OceanDNA-b23099.fa --refList OceanDNA-b23099/target_genomes.txt --output OceanDNA-b23099/fastani_result.tsv --threads 1
[2023-03-15 08:10:36,808] [INFO] Task succeeded: fastANI
[2023-03-15 08:10:36,808] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e594e73-7a21-4aa0-a573-949a060d73ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:10:36,808] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e594e73-7a21-4aa0-a573-949a060d73ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:10:36,820] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:10:36,821] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 08:10:36,821] [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
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	75.2441	144	1343	95	below_threshold
Luteimonas mephitis	strain=DSM 12574	GCA_000422305.1	83615	83615	type	True	75.1348	133	1343	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	75.1221	156	1343	95	below_threshold
Tautonia sociabilis	strain=GM2012	GCA_003977685.1	2080755	2080755	type	True	75.1184	126	1343	95	below_threshold
Arenimonas composti	strain=TR7-09	GCA_000747175.1	370776	370776	type	True	75.0842	205	1343	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	75.0826	206	1343	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	75.0805	190	1343	95	below_threshold
Algisphaera agarilytica	strain=DSM 103725	GCA_014207595.1	1385975	1385975	type	True	75.061	59	1343	95	below_threshold
Humisphaera borealis	strain=M1803	GCA_015169395.1	2807512	2807512	type	True	74.9902	91	1343	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	74.9781	211	1343	95	below_threshold
Myxococcus fulvus	strain=DSM 16525	GCA_900111765.1	33	33	type	True	74.9573	164	1343	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	74.9498	170	1343	95	below_threshold
Myxococcus fulvus	strain=NBRC 100333	GCA_007991095.1	33	33	type	True	74.9322	164	1343	95	below_threshold
Catenulispora pinisilvae	strain=NH11	GCA_015356865.1	2705253	2705253	type	True	74.8102	242	1343	95	below_threshold
Catenulispora acidiphila	strain=DSM 44928	GCA_000024025.1	304895	304895	type	True	74.806	252	1343	95	below_threshold
Streptomyces chattanoogensis	strain=NRRL ISP-5002	GCA_001294335.1	66876	66876	type	True	74.787	164	1343	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	74.7798	167	1343	95	below_threshold
Catenulispora pinistramenti	strain=NL8	GCA_018274385.1	2705254	2705254	type	True	74.7718	232	1343	95	below_threshold
Bradymonas sediminis	strain=FA350	GCA_003258315.1	1548548	1548548	type	True	74.718	54	1343	95	below_threshold
Bradymonas sediminis	strain=DSM 28820	GCA_004362595.1	1548548	1548548	type	True	74.7144	55	1343	95	below_threshold
Micromonospora palomenae	strain=DSM 102131	GCA_007829925.1	1461247	1461247	type	True	74.6842	217	1343	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 08:10:36,821] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23099/tc_result.tsv
[2023-03-15 08:10:36,822] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:10:36,822] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:10:36,822] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e594e73-7a21-4aa0-a573-949a060d73ef/dqc_reference/checkm_data
[2023-03-15 08:10:36,822] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:10:36,829] [INFO] Task started: CheckM
[2023-03-15 08:10:36,829] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23099/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23099/checkm_input OceanDNA-b23099/checkm_result
[2023-03-15 08:11:34,423] [INFO] Task succeeded: CheckM
[2023-03-15 08:11:34,424] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:11:34,427] [INFO] ===== Completeness check finished =====
[2023-03-15 08:11:34,427] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:11:34,427] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23099/markers.fasta)
[2023-03-15 08:11:34,428] [INFO] Task started: Blastn
[2023-03-15 08:11:34,428] [INFO] Running command: blastn -query OceanDNA-b23099/markers.fasta -db /var/lib/cwl/stg8e594e73-7a21-4aa0-a573-949a060d73ef/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23099/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:11:35,683] [INFO] Task succeeded: Blastn
[2023-03-15 08:11:35,684] [INFO] Selected 10 target genomes.
[2023-03-15 08:11:35,684] [INFO] Target genome list was writen to OceanDNA-b23099/target_genomes_gtdb.txt
[2023-03-15 08:11:35,689] [INFO] Task started: fastANI
[2023-03-15 08:11:35,690] [INFO] Running command: fastANI --query /var/lib/cwl/stg73116b7d-2785-4e3c-b334-83e41633881b/OceanDNA-b23099.fa --refList OceanDNA-b23099/target_genomes_gtdb.txt --output OceanDNA-b23099/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:11:45,143] [INFO] Task succeeded: fastANI
[2023-03-15 08:11:45,149] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 08:11:45,149] [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_002684655.1	s__GCA-2684655 sp002684655	81.3342	725	1343	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__GCA-2684655	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051855.1	s__GCA-2684655 sp011051855	80.6324	573	1343	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__GCA-2684655	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794035.1	s__JAEUHS01 sp016794035	79.8703	700	1343	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__JAEUHS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794425.1	s__JAEUHS01 sp016794425	79.8488	724	1343	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__JAEUHS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872675.1	s__UBA2386 sp016872675	79.7365	638	1343	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__UBA2386	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793265.1	s__UBA2386 sp016793265	79.6553	662	1343	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__UBA2386	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793305.1	s__UBA2386 sp016793305	79.2519	591	1343	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__UBA2386	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873195.1	s__VGXW01 sp016873195	79.2132	557	1343	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__VGXW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794485.1	s__UBA2386 sp016794485	79.131	603	1343	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__UBA2386	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005776475.1	s__UBA2386 sp005776475	78.4644	539	1343	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__UBA2386	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 08:11:45,150] [INFO] GTDB search result was written to OceanDNA-b23099/result_gtdb.tsv
[2023-03-15 08:11:45,150] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:11:45,151] [INFO] DFAST_QC result json was written to OceanDNA-b23099/dqc_result.json
[2023-03-15 08:11:45,152] [INFO] DFAST_QC completed!
[2023-03-15 08:11:45,152] [INFO] Total running time: 0h1m60s