[2023-03-18 00:35:04,578] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:35:04,578] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:35:04,578] [INFO] DQC Reference Directory: /var/lib/cwl/stg52b3496e-2e14-4c96-a416-fc36f302040e/dqc_reference
[2023-03-18 00:35:05,719] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:35:05,719] [INFO] Task started: Prodigal
[2023-03-18 00:35:05,720] [INFO] Running command: cat /var/lib/cwl/stge4c42e7f-273c-4e0b-b8f5-536fa694dd10/OceanDNA-b8077.fa | prodigal -d OceanDNA-b8077/cds.fna -a OceanDNA-b8077/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:35:11,368] [INFO] Task succeeded: Prodigal
[2023-03-18 00:35:11,368] [INFO] Task started: HMMsearch
[2023-03-18 00:35:11,368] [INFO] Running command: hmmsearch --tblout OceanDNA-b8077/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52b3496e-2e14-4c96-a416-fc36f302040e/dqc_reference/reference_markers.hmm OceanDNA-b8077/protein.faa > /dev/null
[2023-03-18 00:35:11,521] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:35:11,522] [WARNING] Found 3/6 markers. [/var/lib/cwl/stge4c42e7f-273c-4e0b-b8f5-536fa694dd10/OceanDNA-b8077.fa]
[2023-03-18 00:35:11,529] [INFO] Query marker FASTA was written to OceanDNA-b8077/markers.fasta
[2023-03-18 00:35:11,530] [INFO] Task started: Blastn
[2023-03-18 00:35:11,530] [INFO] Running command: blastn -query OceanDNA-b8077/markers.fasta -db /var/lib/cwl/stg52b3496e-2e14-4c96-a416-fc36f302040e/dqc_reference/reference_markers.fasta -out OceanDNA-b8077/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:35:12,022] [INFO] Task succeeded: Blastn
[2023-03-18 00:35:12,023] [INFO] Selected 10 target genomes.
[2023-03-18 00:35:12,023] [INFO] Target genome list was writen to OceanDNA-b8077/target_genomes.txt
[2023-03-18 00:35:12,028] [INFO] Task started: fastANI
[2023-03-18 00:35:12,028] [INFO] Running command: fastANI --query /var/lib/cwl/stge4c42e7f-273c-4e0b-b8f5-536fa694dd10/OceanDNA-b8077.fa --refList OceanDNA-b8077/target_genomes.txt --output OceanDNA-b8077/fastani_result.tsv --threads 1
[2023-03-18 00:35:18,045] [INFO] Task succeeded: fastANI
[2023-03-18 00:35:18,045] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52b3496e-2e14-4c96-a416-fc36f302040e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:35:18,045] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52b3496e-2e14-4c96-a416-fc36f302040e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:35:18,046] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:35:18,046] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:35:18,046] [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
--------------------------------------------------------------------------------
[2023-03-18 00:35:18,046] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8077/tc_result.tsv
[2023-03-18 00:35:18,046] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:35:18,046] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:35:18,046] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52b3496e-2e14-4c96-a416-fc36f302040e/dqc_reference/checkm_data
[2023-03-18 00:35:18,049] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:35:18,056] [INFO] Task started: CheckM
[2023-03-18 00:35:18,056] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8077/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8077/checkm_input OceanDNA-b8077/checkm_result
[2023-03-18 00:35:37,955] [INFO] Task succeeded: CheckM
[2023-03-18 00:35:37,955] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.09%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:35:37,957] [INFO] ===== Completeness check finished =====
[2023-03-18 00:35:37,957] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:35:37,957] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8077/markers.fasta)
[2023-03-18 00:35:37,957] [INFO] Task started: Blastn
[2023-03-18 00:35:37,958] [INFO] Running command: blastn -query OceanDNA-b8077/markers.fasta -db /var/lib/cwl/stg52b3496e-2e14-4c96-a416-fc36f302040e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8077/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:35:38,616] [INFO] Task succeeded: Blastn
[2023-03-18 00:35:38,617] [INFO] Selected 11 target genomes.
[2023-03-18 00:35:38,617] [INFO] Target genome list was writen to OceanDNA-b8077/target_genomes_gtdb.txt
[2023-03-18 00:35:38,626] [INFO] Task started: fastANI
[2023-03-18 00:35:38,626] [INFO] Running command: fastANI --query /var/lib/cwl/stge4c42e7f-273c-4e0b-b8f5-536fa694dd10/OceanDNA-b8077.fa --refList OceanDNA-b8077/target_genomes_gtdb.txt --output OceanDNA-b8077/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:35:41,607] [INFO] Task succeeded: fastANI
[2023-03-18 00:35:41,613] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:35:41,614] [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_905181625.1	s__MAG-121220-bin8 sp905181625	85.3509	270	302	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012959395.1	s__MAG-121220-bin8 sp012959395	82.5486	184	302	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	97.96	97.81	0.81	0.77	13	-
GCA_014239275.1	s__MAG-121220-bin8 sp014239275	78.3489	130	302	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.08	98.67	0.74	0.67	4	-
GCA_902511755.1	s__MAG-121220-bin8 sp902511755	78.0723	114	302	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.22	98.71	0.74	0.72	3	-
GCA_905182765.1	s__MAG-121220-bin8 sp905182765	77.5774	113	302	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002702895.1	s__MAG-121220-bin8 sp002702895	77.4467	127	302	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018662905.1	s__MAG-121220-bin8 sp018662905	77.3238	75	302	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.06	99.06	0.75	0.75	2	-
GCA_003331265.1	s__MAG-121220-bin8 sp003331265	77.2299	107	302	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700465.1	s__MAG-121220-bin8 sp002700465	77.2135	79	302	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.15	98.67	0.80	0.80	3	-
GCA_902559035.1	s__MAG-121220-bin8 sp902559035	77.0744	95	302	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	96.40	96.04	0.82	0.79	6	-
--------------------------------------------------------------------------------
[2023-03-18 00:35:41,614] [INFO] GTDB search result was written to OceanDNA-b8077/result_gtdb.tsv
[2023-03-18 00:35:41,614] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:35:41,615] [INFO] DFAST_QC result json was written to OceanDNA-b8077/dqc_result.json
[2023-03-18 00:35:41,615] [INFO] DFAST_QC completed!
[2023-03-18 00:35:41,615] [INFO] Total running time: 0h0m37s