[2023-03-16 22:45:35,371] [INFO] DFAST_QC pipeline started.
[2023-03-16 22:45:35,372] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 22:45:35,372] [INFO] DQC Reference Directory: /var/lib/cwl/stge2164734-c566-4a45-8211-752a2b5e1cee/dqc_reference
[2023-03-16 22:45:37,282] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 22:45:37,282] [INFO] Task started: Prodigal
[2023-03-16 22:45:37,283] [INFO] Running command: cat /var/lib/cwl/stge375dbc5-d7ac-4207-be12-cde9a849c44c/OceanDNA-a2899.fa | prodigal -d OceanDNA-a2899/cds.fna -a OceanDNA-a2899/protein.faa -g 11 -q > /dev/null
[2023-03-16 22:45:50,023] [INFO] Task succeeded: Prodigal
[2023-03-16 22:45:50,023] [INFO] Task started: HMMsearch
[2023-03-16 22:45:50,023] [INFO] Running command: hmmsearch --tblout OceanDNA-a2899/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2164734-c566-4a45-8211-752a2b5e1cee/dqc_reference/reference_markers.hmm OceanDNA-a2899/protein.faa > /dev/null
[2023-03-16 22:45:50,183] [INFO] Task succeeded: HMMsearch
[2023-03-16 22:45:50,183] [WARNING] Found 3/6 markers. [/var/lib/cwl/stge375dbc5-d7ac-4207-be12-cde9a849c44c/OceanDNA-a2899.fa]
[2023-03-16 22:45:50,196] [INFO] Query marker FASTA was written to OceanDNA-a2899/markers.fasta
[2023-03-16 22:45:50,196] [INFO] Task started: Blastn
[2023-03-16 22:45:50,196] [INFO] Running command: blastn -query OceanDNA-a2899/markers.fasta -db /var/lib/cwl/stge2164734-c566-4a45-8211-752a2b5e1cee/dqc_reference/reference_markers.fasta -out OceanDNA-a2899/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 22:45:50,626] [INFO] Task succeeded: Blastn
[2023-03-16 22:45:50,627] [INFO] Selected 10 target genomes.
[2023-03-16 22:45:50,627] [INFO] Target genome list was writen to OceanDNA-a2899/target_genomes.txt
[2023-03-16 22:45:50,633] [INFO] Task started: fastANI
[2023-03-16 22:45:50,633] [INFO] Running command: fastANI --query /var/lib/cwl/stge375dbc5-d7ac-4207-be12-cde9a849c44c/OceanDNA-a2899.fa --refList OceanDNA-a2899/target_genomes.txt --output OceanDNA-a2899/fastani_result.tsv --threads 1
[2023-03-16 22:45:56,457] [INFO] Task succeeded: fastANI
[2023-03-16 22:45:56,458] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2164734-c566-4a45-8211-752a2b5e1cee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 22:45:56,458] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2164734-c566-4a45-8211-752a2b5e1cee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 22:45:56,458] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 22:45:56,458] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 22:45:56,458] [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
--------------------------------------------------------------------------------
[2023-03-16 22:45:56,458] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2899/tc_result.tsv
[2023-03-16 22:45:56,459] [INFO] ===== Taxonomy check completed =====
[2023-03-16 22:45:56,459] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 22:45:56,459] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2164734-c566-4a45-8211-752a2b5e1cee/dqc_reference/checkm_data
[2023-03-16 22:45:56,461] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 22:45:56,464] [INFO] Task started: CheckM
[2023-03-16 22:45:56,464] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2899/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2899/checkm_input OceanDNA-a2899/checkm_result
[2023-03-16 22:46:45,250] [INFO] Task succeeded: CheckM
[2023-03-16 22:46:45,250] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.28%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 22:46:45,252] [INFO] ===== Completeness check finished =====
[2023-03-16 22:46:45,252] [INFO] ===== Start GTDB Search =====
[2023-03-16 22:46:45,252] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2899/markers.fasta)
[2023-03-16 22:46:45,254] [INFO] Task started: Blastn
[2023-03-16 22:46:45,254] [INFO] Running command: blastn -query OceanDNA-a2899/markers.fasta -db /var/lib/cwl/stge2164734-c566-4a45-8211-752a2b5e1cee/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2899/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 22:46:45,688] [INFO] Task succeeded: Blastn
[2023-03-16 22:46:45,688] [INFO] Selected 8 target genomes.
[2023-03-16 22:46:45,688] [INFO] Target genome list was writen to OceanDNA-a2899/target_genomes_gtdb.txt
[2023-03-16 22:46:46,033] [INFO] Task started: fastANI
[2023-03-16 22:46:46,034] [INFO] Running command: fastANI --query /var/lib/cwl/stge375dbc5-d7ac-4207-be12-cde9a849c44c/OceanDNA-a2899.fa --refList OceanDNA-a2899/target_genomes_gtdb.txt --output OceanDNA-a2899/fastani_result_gtdb.tsv --threads 1
[2023-03-16 22:46:48,836] [INFO] Task succeeded: fastANI
[2023-03-16 22:46:48,841] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 22:46:48,841] [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_002722135.1	s__MGIIa-L3 sp002722135	99.663	571	608	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L3	95.0	99.74	99.72	0.92	0.89	4	conclusive
GCA_002694585.1	s__MGIIa-L3 sp002694585	92.9577	453	608	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002731395.1	s__MGIIa-L3 sp002731395	85.3694	396	608	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L3	95.0	99.15	99.02	0.81	0.76	3	-
GCA_003602635.1	s__MGIIa-L3 sp003602635	82.9785	354	608	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013330925.1	s__MGIIa-L3 sp11892u	82.167	326	608	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L3	95.0	99.55	99.23	0.93	0.88	5	-
GCA_013330765.1	s__MGIIa-L3 sp12206u	80.9128	265	608	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L3	95.0	100.00	100.00	0.99	0.99	2	-
GCA_002497765.1	s__Poseidonia sp002497765	78.0949	98	608	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.70	99.65	0.88	0.86	3	-
GCA_002714305.1	s__Poseidonia sp002714305	76.767	51	608	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	98.69	98.28	0.79	0.76	8	-
--------------------------------------------------------------------------------
[2023-03-16 22:46:48,842] [INFO] GTDB search result was written to OceanDNA-a2899/result_gtdb.tsv
[2023-03-16 22:46:48,842] [INFO] ===== GTDB Search completed =====
[2023-03-16 22:46:48,842] [INFO] DFAST_QC result json was written to OceanDNA-a2899/dqc_result.json
[2023-03-16 22:46:48,843] [INFO] DFAST_QC completed!
[2023-03-16 22:46:48,843] [INFO] Total running time: 0h1m13s