[2023-03-18 01:41:20,928] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:41:20,928] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:41:20,928] [INFO] DQC Reference Directory: /var/lib/cwl/stg25a8f62c-1f28-48ed-a6d1-09fef90c6531/dqc_reference
[2023-03-18 01:41:22,162] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:41:22,163] [INFO] Task started: Prodigal
[2023-03-18 01:41:22,163] [INFO] Running command: cat /var/lib/cwl/stg7c3e698c-8b2e-44c4-8c6a-84f3fbecaf92/OceanDNA-b22084.fa | prodigal -d OceanDNA-b22084/cds.fna -a OceanDNA-b22084/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:41:31,720] [INFO] Task succeeded: Prodigal
[2023-03-18 01:41:31,721] [INFO] Task started: HMMsearch
[2023-03-18 01:41:31,721] [INFO] Running command: hmmsearch --tblout OceanDNA-b22084/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25a8f62c-1f28-48ed-a6d1-09fef90c6531/dqc_reference/reference_markers.hmm OceanDNA-b22084/protein.faa > /dev/null
[2023-03-18 01:41:31,899] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:41:31,900] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7c3e698c-8b2e-44c4-8c6a-84f3fbecaf92/OceanDNA-b22084.fa]
[2023-03-18 01:41:31,917] [INFO] Query marker FASTA was written to OceanDNA-b22084/markers.fasta
[2023-03-18 01:41:31,918] [INFO] Task started: Blastn
[2023-03-18 01:41:31,919] [INFO] Running command: blastn -query OceanDNA-b22084/markers.fasta -db /var/lib/cwl/stg25a8f62c-1f28-48ed-a6d1-09fef90c6531/dqc_reference/reference_markers.fasta -out OceanDNA-b22084/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:41:32,671] [INFO] Task succeeded: Blastn
[2023-03-18 01:41:32,671] [INFO] Selected 17 target genomes.
[2023-03-18 01:41:32,672] [INFO] Target genome list was writen to OceanDNA-b22084/target_genomes.txt
[2023-03-18 01:41:32,686] [INFO] Task started: fastANI
[2023-03-18 01:41:32,687] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c3e698c-8b2e-44c4-8c6a-84f3fbecaf92/OceanDNA-b22084.fa --refList OceanDNA-b22084/target_genomes.txt --output OceanDNA-b22084/fastani_result.tsv --threads 1
[2023-03-18 01:41:46,139] [INFO] Task succeeded: fastANI
[2023-03-18 01:41:46,140] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25a8f62c-1f28-48ed-a6d1-09fef90c6531/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:41:46,140] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25a8f62c-1f28-48ed-a6d1-09fef90c6531/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:41:46,147] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:41:46,147] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:41:46,147] [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
Algisphaera agarilytica	strain=DSM 103725	GCA_014207595.1	1385975	1385975	type	True	79.0801	234	454	95	below_threshold
Mucisphaera calidilacus	strain=Pan265	GCA_007748075.1	2527982	2527982	type	True	76.8612	60	454	95	below_threshold
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	76.4953	136	454	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	76.4549	138	454	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	74.9671	58	454	95	below_threshold
Geodermatophilus poikilotrophus	strain=DSM 44209	GCA_900111455.1	1333667	1333667	type	True	74.9067	55	454	95	below_threshold
Geodermatophilus siccatus	strain=DSM 45419	GCA_900103785.1	1137991	1137991	type	True	74.8886	54	454	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	74.8274	64	454	95	below_threshold
Actinomycetospora corticicola	strain=DSM 45772	GCA_013409505.1	663602	663602	type	True	74.7699	68	454	95	below_threshold
Cryptosporangium phraense	strain=A-T 5661	GCA_006912135.1	2593070	2593070	type	True	74.7639	52	454	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:41:46,147] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22084/tc_result.tsv
[2023-03-18 01:41:46,147] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:41:46,147] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:41:46,147] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25a8f62c-1f28-48ed-a6d1-09fef90c6531/dqc_reference/checkm_data
[2023-03-18 01:41:46,148] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:41:46,152] [INFO] Task started: CheckM
[2023-03-18 01:41:46,152] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22084/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22084/checkm_input OceanDNA-b22084/checkm_result
[2023-03-18 01:42:14,206] [INFO] Task succeeded: CheckM
[2023-03-18 01:42:14,206] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.91%
Contamintation: 1.56%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 01:42:14,208] [INFO] ===== Completeness check finished =====
[2023-03-18 01:42:14,209] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:42:14,209] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22084/markers.fasta)
[2023-03-18 01:42:14,210] [INFO] Task started: Blastn
[2023-03-18 01:42:14,210] [INFO] Running command: blastn -query OceanDNA-b22084/markers.fasta -db /var/lib/cwl/stg25a8f62c-1f28-48ed-a6d1-09fef90c6531/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22084/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:42:15,141] [INFO] Task succeeded: Blastn
[2023-03-18 01:42:15,142] [INFO] Selected 18 target genomes.
[2023-03-18 01:42:15,142] [INFO] Target genome list was writen to OceanDNA-b22084/target_genomes_gtdb.txt
[2023-03-18 01:42:15,162] [INFO] Task started: fastANI
[2023-03-18 01:42:15,162] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c3e698c-8b2e-44c4-8c6a-84f3fbecaf92/OceanDNA-b22084.fa --refList OceanDNA-b22084/target_genomes_gtdb.txt --output OceanDNA-b22084/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:42:26,311] [INFO] Task succeeded: fastANI
[2023-03-18 01:42:26,317] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:42:26,317] [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
GCF_014207595.1	s__Algisphaera agarilytica	79.0801	234	454	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__Algisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007748075.1	s__Pan265 sp007748075	76.8638	60	454	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__Pan265	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284115.1	s__Phycisphaera mikurensis	76.4666	138	454	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__Phycisphaera	95.0	99.99	99.99	1.00	1.00	2	-
GCA_016125215.1	s__RI-382 sp016125215	76.4299	75	454	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__RI-382	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007119405.1	s__SKPT01 sp007119405	76.1988	60	454	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__SKPT01	95.0	98.45	98.45	0.84	0.84	2	-
GCA_003551485.1	s__B1Sed10-187 sp003551485	76.176	68	454	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__B1Sed10-187	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003696725.1	s__J020 sp003696725	75.5556	53	454	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__J020	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686995.1	s__GCA-2686995 sp002686995	75.408	68	454	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__GCA-2686995	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125255.1	s__RI-421 sp016125255	75.3876	56	454	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Zrk34;g__RI-421	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:42:26,317] [INFO] GTDB search result was written to OceanDNA-b22084/result_gtdb.tsv
[2023-03-18 01:42:26,317] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:42:26,318] [INFO] DFAST_QC result json was written to OceanDNA-b22084/dqc_result.json
[2023-03-18 01:42:26,318] [INFO] DFAST_QC completed!
[2023-03-18 01:42:26,318] [INFO] Total running time: 0h1m5s