[2023-03-19 04:49:27,638] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:49:27,639] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:49:27,639] [INFO] DQC Reference Directory: /var/lib/cwl/stga59d700f-f0e6-4587-be9f-6724f845985f/dqc_reference
[2023-03-19 04:49:28,749] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:49:28,750] [INFO] Task started: Prodigal
[2023-03-19 04:49:28,750] [INFO] Running command: cat /var/lib/cwl/stg44923e22-9a15-4ac3-838e-6a48ac88cf81/OceanDNA-b13546.fa | prodigal -d OceanDNA-b13546/cds.fna -a OceanDNA-b13546/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:49:51,618] [INFO] Task succeeded: Prodigal
[2023-03-19 04:49:51,618] [INFO] Task started: HMMsearch
[2023-03-19 04:49:51,619] [INFO] Running command: hmmsearch --tblout OceanDNA-b13546/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga59d700f-f0e6-4587-be9f-6724f845985f/dqc_reference/reference_markers.hmm OceanDNA-b13546/protein.faa > /dev/null
[2023-03-19 04:49:51,859] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:49:51,860] [INFO] Found 6/6 markers.
[2023-03-19 04:49:51,885] [INFO] Query marker FASTA was written to OceanDNA-b13546/markers.fasta
[2023-03-19 04:49:51,887] [INFO] Task started: Blastn
[2023-03-19 04:49:51,887] [INFO] Running command: blastn -query OceanDNA-b13546/markers.fasta -db /var/lib/cwl/stga59d700f-f0e6-4587-be9f-6724f845985f/dqc_reference/reference_markers.fasta -out OceanDNA-b13546/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:49:52,395] [INFO] Task succeeded: Blastn
[2023-03-19 04:49:52,396] [INFO] Selected 20 target genomes.
[2023-03-19 04:49:52,396] [INFO] Target genome list was writen to OceanDNA-b13546/target_genomes.txt
[2023-03-19 04:49:52,435] [INFO] Task started: fastANI
[2023-03-19 04:49:52,435] [INFO] Running command: fastANI --query /var/lib/cwl/stg44923e22-9a15-4ac3-838e-6a48ac88cf81/OceanDNA-b13546.fa --refList OceanDNA-b13546/target_genomes.txt --output OceanDNA-b13546/fastani_result.tsv --threads 1
[2023-03-19 04:50:04,015] [INFO] Task succeeded: fastANI
[2023-03-19 04:50:04,016] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga59d700f-f0e6-4587-be9f-6724f845985f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:50:04,016] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga59d700f-f0e6-4587-be9f-6724f845985f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:50:04,016] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:50:04,016] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:50:04,016] [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
--------------------------------------------------------------------------------
[2023-03-19 04:50:04,016] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13546/tc_result.tsv
[2023-03-19 04:50:04,017] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:50:04,017] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:50:04,017] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga59d700f-f0e6-4587-be9f-6724f845985f/dqc_reference/checkm_data
[2023-03-19 04:50:04,020] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:50:04,025] [INFO] Task started: CheckM
[2023-03-19 04:50:04,025] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13546/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13546/checkm_input OceanDNA-b13546/checkm_result
[2023-03-19 04:51:01,543] [INFO] Task succeeded: CheckM
[2023-03-19 04:51:01,544] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:51:01,572] [INFO] ===== Completeness check finished =====
[2023-03-19 04:51:01,572] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:51:01,572] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13546/markers.fasta)
[2023-03-19 04:51:01,573] [INFO] Task started: Blastn
[2023-03-19 04:51:01,573] [INFO] Running command: blastn -query OceanDNA-b13546/markers.fasta -db /var/lib/cwl/stga59d700f-f0e6-4587-be9f-6724f845985f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13546/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:51:02,269] [INFO] Task succeeded: Blastn
[2023-03-19 04:51:02,270] [INFO] Selected 20 target genomes.
[2023-03-19 04:51:02,270] [INFO] Target genome list was writen to OceanDNA-b13546/target_genomes_gtdb.txt
[2023-03-19 04:51:02,299] [INFO] Task started: fastANI
[2023-03-19 04:51:02,300] [INFO] Running command: fastANI --query /var/lib/cwl/stg44923e22-9a15-4ac3-838e-6a48ac88cf81/OceanDNA-b13546.fa --refList OceanDNA-b13546/target_genomes_gtdb.txt --output OceanDNA-b13546/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:51:16,316] [INFO] Task succeeded: fastANI
[2023-03-19 04:51:16,320] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:51:16,320] [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_018645405.1	s__Desulfolinea sp018645405	99.8357	1093	1307	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__Desulfolinea	95.0	99.86	99.73	0.91	0.78	10	conclusive
GCA_016744335.1	s__Desulfolinea sp016744335	80.2092	431	1307	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__Desulfolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018648655.1	s__Desulfolinea sp018648655	80.0455	433	1307	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__Desulfolinea	95.0	99.77	99.77	0.84	0.82	3	-
GCA_018648685.1	s__Desulfolinea sp018648685	79.5653	463	1307	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__Desulfolinea	95.0	99.60	99.55	0.84	0.83	3	-
GCA_018648605.1	s__Desulfolinea sp018648605	79.2229	373	1307	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__Desulfolinea	95.0	99.90	99.89	0.94	0.91	3	-
GCA_014382535.1	s__Desulfolinea nitratireducens	77.9991	288	1307	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__Desulfolinea	95.0	99.72	99.72	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-03-19 04:51:16,321] [INFO] GTDB search result was written to OceanDNA-b13546/result_gtdb.tsv
[2023-03-19 04:51:16,321] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:51:16,322] [INFO] DFAST_QC result json was written to OceanDNA-b13546/dqc_result.json
[2023-03-19 04:51:16,323] [INFO] DFAST_QC completed!
[2023-03-19 04:51:16,323] [INFO] Total running time: 0h1m49s