[2023-03-18 02:42:32,873] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:42:32,873] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:42:32,873] [INFO] DQC Reference Directory: /var/lib/cwl/stgaab53635-1e2c-449d-af71-d9111ad2ed09/dqc_reference
[2023-03-18 02:42:34,115] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:42:34,116] [INFO] Task started: Prodigal
[2023-03-18 02:42:34,117] [INFO] Running command: cat /var/lib/cwl/stg6627e3d7-4039-4629-a88a-a96e607504b0/OceanDNA-b3405.fa | prodigal -d OceanDNA-b3405/cds.fna -a OceanDNA-b3405/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:42:59,730] [INFO] Task succeeded: Prodigal
[2023-03-18 02:42:59,730] [INFO] Task started: HMMsearch
[2023-03-18 02:42:59,730] [INFO] Running command: hmmsearch --tblout OceanDNA-b3405/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaab53635-1e2c-449d-af71-d9111ad2ed09/dqc_reference/reference_markers.hmm OceanDNA-b3405/protein.faa > /dev/null
[2023-03-18 02:42:59,945] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:42:59,945] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6627e3d7-4039-4629-a88a-a96e607504b0/OceanDNA-b3405.fa]
[2023-03-18 02:42:59,968] [INFO] Query marker FASTA was written to OceanDNA-b3405/markers.fasta
[2023-03-18 02:42:59,969] [INFO] Task started: Blastn
[2023-03-18 02:42:59,969] [INFO] Running command: blastn -query OceanDNA-b3405/markers.fasta -db /var/lib/cwl/stgaab53635-1e2c-449d-af71-d9111ad2ed09/dqc_reference/reference_markers.fasta -out OceanDNA-b3405/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:43:00,869] [INFO] Task succeeded: Blastn
[2023-03-18 02:43:00,870] [INFO] Selected 22 target genomes.
[2023-03-18 02:43:00,870] [INFO] Target genome list was writen to OceanDNA-b3405/target_genomes.txt
[2023-03-18 02:43:00,880] [INFO] Task started: fastANI
[2023-03-18 02:43:00,880] [INFO] Running command: fastANI --query /var/lib/cwl/stg6627e3d7-4039-4629-a88a-a96e607504b0/OceanDNA-b3405.fa --refList OceanDNA-b3405/target_genomes.txt --output OceanDNA-b3405/fastani_result.tsv --threads 1
[2023-03-18 02:43:21,043] [INFO] Task succeeded: fastANI
[2023-03-18 02:43:21,044] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaab53635-1e2c-449d-af71-d9111ad2ed09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:43:21,044] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaab53635-1e2c-449d-af71-d9111ad2ed09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:43:21,056] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:43:21,056] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 02:43:21,056] [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
Nocardioides rubriscoriae	strain=DSM 23986	GCA_008087085.1	642762	642762	type	True	82.1081	897	1413	95	below_threshold
Nocardioides plantarum	strain=DSM 11054	GCA_006346395.1	29299	29299	type	True	81.8199	856	1413	95	below_threshold
Nocardioides litoris	strain=DSM 103718	GCA_006346315.1	1926648	1926648	type	True	81.5594	838	1413	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013409965.1	419476	419476	type	True	81.2155	782	1413	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_016907435.1	374513	374513	type	True	81.2147	774	1413	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	81.2075	769	1413	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015070765.1	374513	374513	type	True	81.1814	786	1413	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	81.1754	786	1413	95	below_threshold
Nocardioides lijunqiniae	strain=S-531	GCA_015024225.1	2760832	2760832	type	True	81.1529	808	1413	95	below_threshold
Nocardioides szechwanensis	strain=CGMCC 1.11147	GCA_900103935.1	1005944	1005944	type	True	81.0758	794	1413	95	below_threshold
Nocardioides szechwanensis	strain=NBRC 108562	GCA_007992395.1	1005944	1005944	type	True	81.0678	788	1413	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	80.7945	730	1413	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	80.7445	797	1413	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	80.7033	734	1413	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_013409225.1	1045774	1045774	type	True	80.6862	813	1413	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	80.4927	683	1413	95	below_threshold
Nocardioides sediminis	strain=KCTC 19271	GCA_003047295.1	433648	433648	type	True	80.0656	648	1413	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	79.9296	590	1413	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	79.8693	649	1413	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	79.8614	641	1413	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	79.7473	646	1413	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	79.6417	680	1413	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 02:43:21,056] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3405/tc_result.tsv
[2023-03-18 02:43:21,056] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:43:21,056] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:43:21,057] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaab53635-1e2c-449d-af71-d9111ad2ed09/dqc_reference/checkm_data
[2023-03-18 02:43:21,057] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:43:21,163] [INFO] Task started: CheckM
[2023-03-18 02:43:21,163] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3405/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3405/checkm_input OceanDNA-b3405/checkm_result
[2023-03-18 02:44:46,752] [INFO] Task succeeded: CheckM
[2023-03-18 02:44:46,752] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:44:46,755] [INFO] ===== Completeness check finished =====
[2023-03-18 02:44:46,755] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:44:46,756] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3405/markers.fasta)
[2023-03-18 02:44:46,756] [INFO] Task started: Blastn
[2023-03-18 02:44:46,756] [INFO] Running command: blastn -query OceanDNA-b3405/markers.fasta -db /var/lib/cwl/stgaab53635-1e2c-449d-af71-d9111ad2ed09/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3405/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:44:48,200] [INFO] Task succeeded: Blastn
[2023-03-18 02:44:48,201] [INFO] Selected 15 target genomes.
[2023-03-18 02:44:48,201] [INFO] Target genome list was writen to OceanDNA-b3405/target_genomes_gtdb.txt
[2023-03-18 02:44:48,377] [INFO] Task started: fastANI
[2023-03-18 02:44:48,377] [INFO] Running command: fastANI --query /var/lib/cwl/stg6627e3d7-4039-4629-a88a-a96e607504b0/OceanDNA-b3405.fa --refList OceanDNA-b3405/target_genomes_gtdb.txt --output OceanDNA-b3405/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:45:03,438] [INFO] Task succeeded: fastANI
[2023-03-18 02:45:03,447] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 02:45:03,447] [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_002698575.1	s__Nocardioides sp002698575	98.9429	1112	1413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008087085.1	s__Nocardioides rubriscoriae	82.0744	901	1413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004522105.1	s__Nocardioides sp004522105	81.7116	826	1413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006346315.1	s__Nocardioides litoris	81.557	838	1413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907435.1	s__Nocardioides salarius	81.2135	774	1413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	3	-
GCF_013466785.1	s__Nocardioides marinisabuli	81.2102	769	1413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_015024225.1	s__Nocardioides sp015024225	81.1471	809	1413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.48	97.48	0.91	0.91	2	-
GCF_004522095.1	s__Nocardioides sp004522095	81.1323	823	1413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103935.1	s__Nocardioides szechwanensis	81.0861	792	1413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002117935.1	s__Nocardioides sp002117935	80.9252	746	1413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001653335.1	s__Nocardioides dokdonensis	80.9242	746	1413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013177455.1	s__Nocardioides sp013177455	80.8836	737	1413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
GCF_900101465.1	s__Nocardioides lianchengensis	80.7602	795	1413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013778305.1	s__Nocardioides sp013778305	80.6527	714	1413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011420305.2	s__Nocardioides sp011420305	80.5001	673	1413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	99.38	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-18 02:45:03,447] [INFO] GTDB search result was written to OceanDNA-b3405/result_gtdb.tsv
[2023-03-18 02:45:03,447] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:45:03,449] [INFO] DFAST_QC result json was written to OceanDNA-b3405/dqc_result.json
[2023-03-18 02:45:03,449] [INFO] DFAST_QC completed!
[2023-03-18 02:45:03,449] [INFO] Total running time: 0h2m31s