[2023-03-19 04:11:06,929] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:11:06,929] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:11:06,929] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f50b01c-f555-408f-81e4-4a19e508af25/dqc_reference
[2023-03-19 04:11:08,641] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:11:08,642] [INFO] Task started: Prodigal
[2023-03-19 04:11:08,642] [INFO] Running command: cat /var/lib/cwl/stg66e62837-066c-4b56-80fd-4046618341d4/OceanDNA-b13076.fa | prodigal -d OceanDNA-b13076/cds.fna -a OceanDNA-b13076/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:11:38,856] [INFO] Task succeeded: Prodigal
[2023-03-19 04:11:38,856] [INFO] Task started: HMMsearch
[2023-03-19 04:11:38,856] [INFO] Running command: hmmsearch --tblout OceanDNA-b13076/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f50b01c-f555-408f-81e4-4a19e508af25/dqc_reference/reference_markers.hmm OceanDNA-b13076/protein.faa > /dev/null
[2023-03-19 04:11:39,071] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:11:39,072] [INFO] Found 6/6 markers.
[2023-03-19 04:11:39,095] [INFO] Query marker FASTA was written to OceanDNA-b13076/markers.fasta
[2023-03-19 04:11:39,095] [INFO] Task started: Blastn
[2023-03-19 04:11:39,095] [INFO] Running command: blastn -query OceanDNA-b13076/markers.fasta -db /var/lib/cwl/stg2f50b01c-f555-408f-81e4-4a19e508af25/dqc_reference/reference_markers.fasta -out OceanDNA-b13076/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:11:39,701] [INFO] Task succeeded: Blastn
[2023-03-19 04:11:39,701] [INFO] Selected 26 target genomes.
[2023-03-19 04:11:39,702] [INFO] Target genome list was writen to OceanDNA-b13076/target_genomes.txt
[2023-03-19 04:11:39,718] [INFO] Task started: fastANI
[2023-03-19 04:11:39,718] [INFO] Running command: fastANI --query /var/lib/cwl/stg66e62837-066c-4b56-80fd-4046618341d4/OceanDNA-b13076.fa --refList OceanDNA-b13076/target_genomes.txt --output OceanDNA-b13076/fastani_result.tsv --threads 1
[2023-03-19 04:11:57,233] [INFO] Task succeeded: fastANI
[2023-03-19 04:11:57,234] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f50b01c-f555-408f-81e4-4a19e508af25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:11:57,234] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f50b01c-f555-408f-81e4-4a19e508af25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:11:57,239] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:11:57,239] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:11:57,239] [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
Rubricoccus marinus	strain=SG-29	GCA_002257665.1	716817	716817	type	True	76.3284	118	1216	95	below_threshold
Rubrivirga marina	strain=SAORIC-28	GCA_002283365.1	1196024	1196024	type	True	76.3047	142	1216	95	below_threshold
Rhodocaloribacter litoris	strain=ISCAR-4553	GCA_011682235.2	2558931	2558931	type	True	76.27	90	1216	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	74.7605	53	1216	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	74.7205	66	1216	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:11:57,239] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13076/tc_result.tsv
[2023-03-19 04:11:57,239] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:11:57,239] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:11:57,239] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f50b01c-f555-408f-81e4-4a19e508af25/dqc_reference/checkm_data
[2023-03-19 04:11:57,240] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:11:57,298] [INFO] Task started: CheckM
[2023-03-19 04:11:57,299] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13076/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13076/checkm_input OceanDNA-b13076/checkm_result
[2023-03-19 04:13:09,504] [INFO] Task succeeded: CheckM
[2023-03-19 04:13:09,504] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:13:09,507] [INFO] ===== Completeness check finished =====
[2023-03-19 04:13:09,507] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:13:09,507] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13076/markers.fasta)
[2023-03-19 04:13:09,507] [INFO] Task started: Blastn
[2023-03-19 04:13:09,507] [INFO] Running command: blastn -query OceanDNA-b13076/markers.fasta -db /var/lib/cwl/stg2f50b01c-f555-408f-81e4-4a19e508af25/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13076/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:13:10,428] [INFO] Task succeeded: Blastn
[2023-03-19 04:13:10,429] [INFO] Selected 22 target genomes.
[2023-03-19 04:13:10,429] [INFO] Target genome list was writen to OceanDNA-b13076/target_genomes_gtdb.txt
[2023-03-19 04:13:10,535] [INFO] Task started: fastANI
[2023-03-19 04:13:10,535] [INFO] Running command: fastANI --query /var/lib/cwl/stg66e62837-066c-4b56-80fd-4046618341d4/OceanDNA-b13076.fa --refList OceanDNA-b13076/target_genomes_gtdb.txt --output OceanDNA-b13076/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:13:23,652] [INFO] Task succeeded: fastANI
[2023-03-19 04:13:23,659] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:13:23,659] [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_014879465.1	s__BA12 sp014879465	76.5952	119	1216	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__BA12;g__BA12	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908885.1	s__JAAAOL01 sp009908885	76.4227	103	1216	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__JAAAOL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002257665.1	s__Rubricoccus marinus	76.3284	118	1216	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002283365.1	s__Rubrivirga marina	76.3047	142	1216	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003285105.1	s__MEBICO9517 sp003285105	76.2572	123	1216	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__MEBIC09517;g__MEBICO9517	95.0	96.96	96.85	0.95	0.94	3	-
GCA_011682235.1	s__ISCAR-4553 sp011682235	76.203	90	1216	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__ISCAR-4553;g__ISCAR-4553	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643395.1	s__JABDJZ01 sp017643395	76.2029	59	1216	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__UBA10348;g__JABDJZ01	95.0	100.00	100.00	1.00	1.00	2	-
GCA_012960515.1	s__Rubricoccus sp012960515	76.1598	114	1216	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012269805.1	s__Rubrivirga sp012269805	76.1507	94	1216	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002283555.1	s__Rubrivirga sp002283555	76.1367	169	1216	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	98.32	98.29	0.93	0.92	3	-
GCA_003023275.1	s__QS-8-64-10 sp003023275	75.6576	57	1216	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__QS-8-64-10	95.0	97.61	97.46	0.68	0.68	3	-
GCA_009908415.1	s__JAAAPH01 sp009908415	75.6433	64	1216	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__JAAAPH01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:13:23,660] [INFO] GTDB search result was written to OceanDNA-b13076/result_gtdb.tsv
[2023-03-19 04:13:23,660] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:13:23,661] [INFO] DFAST_QC result json was written to OceanDNA-b13076/dqc_result.json
[2023-03-19 04:13:23,661] [INFO] DFAST_QC completed!
[2023-03-19 04:13:23,661] [INFO] Total running time: 0h2m17s