[2023-03-16 19:54:52,463] [INFO] DFAST_QC pipeline started.
[2023-03-16 19:54:52,463] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 19:54:52,463] [INFO] DQC Reference Directory: /var/lib/cwl/stg58e7f35a-06eb-4a41-a979-ca7f29738f09/dqc_reference
[2023-03-16 19:54:57,868] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 19:54:57,869] [INFO] Task started: Prodigal
[2023-03-16 19:54:57,869] [INFO] Running command: cat /var/lib/cwl/stg65f963e2-b51b-4e59-92f6-e09b1093f76e/OceanDNA-b1246.fa | prodigal -d OceanDNA-b1246/cds.fna -a OceanDNA-b1246/protein.faa -g 11 -q > /dev/null
[2023-03-16 19:55:11,835] [INFO] Task succeeded: Prodigal
[2023-03-16 19:55:11,836] [INFO] Task started: HMMsearch
[2023-03-16 19:55:11,836] [INFO] Running command: hmmsearch --tblout OceanDNA-b1246/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58e7f35a-06eb-4a41-a979-ca7f29738f09/dqc_reference/reference_markers.hmm OceanDNA-b1246/protein.faa > /dev/null
[2023-03-16 19:55:12,021] [INFO] Task succeeded: HMMsearch
[2023-03-16 19:55:12,021] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg65f963e2-b51b-4e59-92f6-e09b1093f76e/OceanDNA-b1246.fa]
[2023-03-16 19:55:12,032] [INFO] Query marker FASTA was written to OceanDNA-b1246/markers.fasta
[2023-03-16 19:55:12,033] [INFO] Task started: Blastn
[2023-03-16 19:55:12,033] [INFO] Running command: blastn -query OceanDNA-b1246/markers.fasta -db /var/lib/cwl/stg58e7f35a-06eb-4a41-a979-ca7f29738f09/dqc_reference/reference_markers.fasta -out OceanDNA-b1246/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:55:16,154] [INFO] Task succeeded: Blastn
[2023-03-16 19:55:16,155] [INFO] Selected 20 target genomes.
[2023-03-16 19:55:16,155] [INFO] Target genome list was writen to OceanDNA-b1246/target_genomes.txt
[2023-03-16 19:55:16,174] [INFO] Task started: fastANI
[2023-03-16 19:55:16,174] [INFO] Running command: fastANI --query /var/lib/cwl/stg65f963e2-b51b-4e59-92f6-e09b1093f76e/OceanDNA-b1246.fa --refList OceanDNA-b1246/target_genomes.txt --output OceanDNA-b1246/fastani_result.tsv --threads 1
[2023-03-16 19:55:38,111] [INFO] Task succeeded: fastANI
[2023-03-16 19:55:38,112] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58e7f35a-06eb-4a41-a979-ca7f29738f09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 19:55:38,112] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58e7f35a-06eb-4a41-a979-ca7f29738f09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 19:55:38,178] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 19:55:38,178] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 19:55:38,178] [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
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.6851	68	289	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.4227	62	289	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.2781	56	289	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 19:55:38,178] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1246/tc_result.tsv
[2023-03-16 19:55:38,178] [INFO] ===== Taxonomy check completed =====
[2023-03-16 19:55:38,178] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 19:55:38,179] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58e7f35a-06eb-4a41-a979-ca7f29738f09/dqc_reference/checkm_data
[2023-03-16 19:55:38,179] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 19:55:38,326] [INFO] Task started: CheckM
[2023-03-16 19:55:38,326] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1246/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1246/checkm_input OceanDNA-b1246/checkm_result
[2023-03-16 19:56:06,852] [INFO] Task succeeded: CheckM
[2023-03-16 19:56:06,853] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 19:56:06,854] [INFO] ===== Completeness check finished =====
[2023-03-16 19:56:06,855] [INFO] ===== Start GTDB Search =====
[2023-03-16 19:56:06,855] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1246/markers.fasta)
[2023-03-16 19:56:06,856] [INFO] Task started: Blastn
[2023-03-16 19:56:06,856] [INFO] Running command: blastn -query OceanDNA-b1246/markers.fasta -db /var/lib/cwl/stg58e7f35a-06eb-4a41-a979-ca7f29738f09/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1246/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:56:08,050] [INFO] Task succeeded: Blastn
[2023-03-16 19:56:08,050] [INFO] Selected 13 target genomes.
[2023-03-16 19:56:08,050] [INFO] Target genome list was writen to OceanDNA-b1246/target_genomes_gtdb.txt
[2023-03-16 19:56:08,080] [INFO] Task started: fastANI
[2023-03-16 19:56:08,080] [INFO] Running command: fastANI --query /var/lib/cwl/stg65f963e2-b51b-4e59-92f6-e09b1093f76e/OceanDNA-b1246.fa --refList OceanDNA-b1246/target_genomes_gtdb.txt --output OceanDNA-b1246/fastani_result_gtdb.tsv --threads 1
[2023-03-16 19:56:12,912] [INFO] Task succeeded: fastANI
[2023-03-16 19:56:12,919] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 19:56:12,919] [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_012961035.1	s__UBA9410 sp012961035	88.9322	265	289	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	99.67	99.67	0.93	0.93	2	-
GCA_014240365.1	s__UBA9410 sp014240365	86.2517	269	289	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	98.11	98.07	0.86	0.84	5	-
GCA_016845305.1	s__UBA9410 sp016845305	80.4306	213	289	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239855.1	s__UBA9410 sp014239855	79.7923	208	289	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002727895.1	s__UBA9410 sp002727895	79.6642	152	289	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	97.12	97.12	0.93	0.93	2	-
GCA_014237715.1	s__UBA9410 sp014237715	79.2957	176	289	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	98.52	98.52	0.97	0.97	2	-
GCA_018673475.1	s__UBA3125 sp018673475	77.6392	90	289	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA3125	95.0	99.96	99.93	0.97	0.96	16	-
GCA_002687745.1	s__UBA3125 sp002687745	77.4969	82	289	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA3125	95.0	98.98	96.61	0.89	0.87	5	-
GCA_002365325.1	s__UBA3125 sp002365325	77.1961	88	289	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA3125	95.0	98.82	97.98	0.79	0.76	7	-
GCA_003697065.1	s__J010 sp003697065	77.1587	51	289	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__J010	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009835395.1	s__VXNF01 sp009835395	77.0172	58	289	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Bin134;g__VXNF01	95.0	99.94	99.92	0.97	0.97	3	-
--------------------------------------------------------------------------------
[2023-03-16 19:56:12,920] [INFO] GTDB search result was written to OceanDNA-b1246/result_gtdb.tsv
[2023-03-16 19:56:12,920] [INFO] ===== GTDB Search completed =====
[2023-03-16 19:56:12,921] [INFO] DFAST_QC result json was written to OceanDNA-b1246/dqc_result.json
[2023-03-16 19:56:12,921] [INFO] DFAST_QC completed!
[2023-03-16 19:56:12,921] [INFO] Total running time: 0h1m20s