[2023-03-16 04:52:20,155] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:52:20,155] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:52:20,155] [INFO] DQC Reference Directory: /var/lib/cwl/stgf43528ef-2621-4fb7-8cc1-5bae2a4a7a48/dqc_reference
[2023-03-16 04:52:21,246] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:52:21,247] [INFO] Task started: Prodigal
[2023-03-16 04:52:21,247] [INFO] Running command: cat /var/lib/cwl/stg531967c6-4177-4109-a87b-7082e947b894/OceanDNA-b21005.fa | prodigal -d OceanDNA-b21005/cds.fna -a OceanDNA-b21005/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:52:31,313] [INFO] Task succeeded: Prodigal
[2023-03-16 04:52:31,313] [INFO] Task started: HMMsearch
[2023-03-16 04:52:31,314] [INFO] Running command: hmmsearch --tblout OceanDNA-b21005/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf43528ef-2621-4fb7-8cc1-5bae2a4a7a48/dqc_reference/reference_markers.hmm OceanDNA-b21005/protein.faa > /dev/null
[2023-03-16 04:52:31,474] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:52:31,475] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg531967c6-4177-4109-a87b-7082e947b894/OceanDNA-b21005.fa]
[2023-03-16 04:52:31,492] [INFO] Query marker FASTA was written to OceanDNA-b21005/markers.fasta
[2023-03-16 04:52:31,492] [INFO] Task started: Blastn
[2023-03-16 04:52:31,492] [INFO] Running command: blastn -query OceanDNA-b21005/markers.fasta -db /var/lib/cwl/stgf43528ef-2621-4fb7-8cc1-5bae2a4a7a48/dqc_reference/reference_markers.fasta -out OceanDNA-b21005/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:52:32,077] [INFO] Task succeeded: Blastn
[2023-03-16 04:52:32,078] [INFO] Selected 20 target genomes.
[2023-03-16 04:52:32,078] [INFO] Target genome list was writen to OceanDNA-b21005/target_genomes.txt
[2023-03-16 04:52:32,091] [INFO] Task started: fastANI
[2023-03-16 04:52:32,091] [INFO] Running command: fastANI --query /var/lib/cwl/stg531967c6-4177-4109-a87b-7082e947b894/OceanDNA-b21005.fa --refList OceanDNA-b21005/target_genomes.txt --output OceanDNA-b21005/fastani_result.tsv --threads 1
[2023-03-16 04:52:48,708] [INFO] Task succeeded: fastANI
[2023-03-16 04:52:48,708] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf43528ef-2621-4fb7-8cc1-5bae2a4a7a48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:52:48,708] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf43528ef-2621-4fb7-8cc1-5bae2a4a7a48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:52:48,712] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:52:48,712] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:52:48,712] [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
Archangium gephyra	strain=DSM 2261	GCA_003387095.1	48	48	type	True	74.7847	51	508	95	below_threshold
Geodermatophilus normandii	strain=DSM 45417	GCA_003182485.1	1137989	1137989	type	True	74.7511	60	508	95	below_threshold
Micromonospora carbonacea	strain=aurantiaca	GCA_013389765.1	47853	47853	type	True	74.7499	55	508	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:52:48,712] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21005/tc_result.tsv
[2023-03-16 04:52:48,712] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:52:48,712] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:52:48,712] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf43528ef-2621-4fb7-8cc1-5bae2a4a7a48/dqc_reference/checkm_data
[2023-03-16 04:52:48,713] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:52:48,716] [INFO] Task started: CheckM
[2023-03-16 04:52:48,717] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21005/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21005/checkm_input OceanDNA-b21005/checkm_result
[2023-03-16 04:53:17,368] [INFO] Task succeeded: CheckM
[2023-03-16 04:53:17,369] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.71%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:53:17,371] [INFO] ===== Completeness check finished =====
[2023-03-16 04:53:17,371] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:53:17,371] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21005/markers.fasta)
[2023-03-16 04:53:17,371] [INFO] Task started: Blastn
[2023-03-16 04:53:17,371] [INFO] Running command: blastn -query OceanDNA-b21005/markers.fasta -db /var/lib/cwl/stgf43528ef-2621-4fb7-8cc1-5bae2a4a7a48/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21005/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:53:18,332] [INFO] Task succeeded: Blastn
[2023-03-16 04:53:18,333] [INFO] Selected 20 target genomes.
[2023-03-16 04:53:18,333] [INFO] Target genome list was writen to OceanDNA-b21005/target_genomes_gtdb.txt
[2023-03-16 04:53:18,349] [INFO] Task started: fastANI
[2023-03-16 04:53:18,349] [INFO] Running command: fastANI --query /var/lib/cwl/stg531967c6-4177-4109-a87b-7082e947b894/OceanDNA-b21005.fa --refList OceanDNA-b21005/target_genomes_gtdb.txt --output OceanDNA-b21005/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:53:32,022] [INFO] Task succeeded: fastANI
[2023-03-16 04:53:32,030] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:53:32,030] [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_013215565.1	s__JABSQV01 sp013215565	79.2268	118	508	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__SZUA-336;f__SZUA-336;g__JABSQV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875225.1	s__VGRW01 sp016875225	77.4022	157	508	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__SZUA-336;f__SZUA-336;g__VGRW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004356455.1	s__SMWZ01 sp004356455	77.079	75	508	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__SZUA-336;f__SZUA-336;g__SMWZ01	95.0	99.36	99.36	0.81	0.81	2	-
GCA_003247575.1	s__SZUA-336 sp003247575	76.0449	63	508	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__SZUA-336;f__SZUA-336;g__SZUA-336	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576805.1	s__PR03 sp003576805	76.0306	151	508	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__PR03;g__PR03	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002687015.1	s__GCA-2687015 sp002687015	76.0015	90	508	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__GCA-2687015	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875395.1	s__VGRF01 sp016875395	75.9296	98	508	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__VGRF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900696485.1	s__CAADGG01 sp900696485	75.9035	77	508	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__PR03;g__CAADGG01	95.0	99.84	99.84	0.91	0.91	2	-
GCF_000013385.1	s__Anaeromyxobacter dehalogenans_B	75.0605	77	508	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__Anaeromyxobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793245.1	s__JADKAF01 sp016793245	74.9331	60	508	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__JADKAF01;g__JADKAF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213895.1	s__JACQZJ01 sp016213895	74.9003	53	508	d__Bacteria;p__Planctomycetota;c__B15-G4;o__B15-G4;f__JADJEK01;g__JACQZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709145.1	s__JADJEK01 sp016709145	74.795	50	508	d__Bacteria;p__Planctomycetota;c__B15-G4;o__B15-G4;f__JADJEK01;g__JADJEK01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182485.1	s__Geodermatophilus normandii	74.752	60	508	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:53:32,030] [INFO] GTDB search result was written to OceanDNA-b21005/result_gtdb.tsv
[2023-03-16 04:53:32,030] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:53:32,031] [INFO] DFAST_QC result json was written to OceanDNA-b21005/dqc_result.json
[2023-03-16 04:53:32,031] [INFO] DFAST_QC completed!
[2023-03-16 04:53:32,032] [INFO] Total running time: 0h1m12s