[2023-03-18 23:03:14,056] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:03:14,057] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:03:14,057] [INFO] DQC Reference Directory: /var/lib/cwl/stgab3bd6ce-a5b9-42b4-8c00-26f73b3fe0eb/dqc_reference
[2023-03-18 23:03:15,188] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:03:15,189] [INFO] Task started: Prodigal
[2023-03-18 23:03:15,189] [INFO] Running command: cat /var/lib/cwl/stg89f44a70-8a8d-4205-b60a-0eac49d3a285/OceanDNA-b36616.fa | prodigal -d OceanDNA-b36616/cds.fna -a OceanDNA-b36616/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:03:41,165] [INFO] Task succeeded: Prodigal
[2023-03-18 23:03:41,166] [INFO] Task started: HMMsearch
[2023-03-18 23:03:41,166] [INFO] Running command: hmmsearch --tblout OceanDNA-b36616/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab3bd6ce-a5b9-42b4-8c00-26f73b3fe0eb/dqc_reference/reference_markers.hmm OceanDNA-b36616/protein.faa > /dev/null
[2023-03-18 23:03:41,381] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:03:41,381] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg89f44a70-8a8d-4205-b60a-0eac49d3a285/OceanDNA-b36616.fa]
[2023-03-18 23:03:41,411] [INFO] Query marker FASTA was written to OceanDNA-b36616/markers.fasta
[2023-03-18 23:03:41,412] [INFO] Task started: Blastn
[2023-03-18 23:03:41,412] [INFO] Running command: blastn -query OceanDNA-b36616/markers.fasta -db /var/lib/cwl/stgab3bd6ce-a5b9-42b4-8c00-26f73b3fe0eb/dqc_reference/reference_markers.fasta -out OceanDNA-b36616/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:03:42,196] [INFO] Task succeeded: Blastn
[2023-03-18 23:03:42,198] [INFO] Selected 9 target genomes.
[2023-03-18 23:03:42,198] [INFO] Target genome list was writen to OceanDNA-b36616/target_genomes.txt
[2023-03-18 23:03:42,203] [INFO] Task started: fastANI
[2023-03-18 23:03:42,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg89f44a70-8a8d-4205-b60a-0eac49d3a285/OceanDNA-b36616.fa --refList OceanDNA-b36616/target_genomes.txt --output OceanDNA-b36616/fastani_result.tsv --threads 1
[2023-03-18 23:03:50,144] [INFO] Task succeeded: fastANI
[2023-03-18 23:03:50,145] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab3bd6ce-a5b9-42b4-8c00-26f73b3fe0eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:03:50,145] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab3bd6ce-a5b9-42b4-8c00-26f73b3fe0eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:03:50,151] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 23:03:50,152] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 23:03:50,152] [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
Alcanivorax xenomutans	strain=JC109	GCA_900217905.1	1094342	1094342	type	True	98.3774	1239	1355	95	conclusive
Alcanivorax balearicus	strain=MACL04	GCA_025532145.1	413232	413232	type	True	94.6118	1224	1355	95	below_threshold
Alcanivorax dieselolei	strain=CGMCC 1.3690	GCA_014644575.1	285091	285091	type	True	93.6734	1219	1355	95	below_threshold
Alcanivorax dieselolei	strain=B5	GCA_000300005.1	285091	285091	type	True	93.6494	1220	1355	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	80.313	602	1355	95	below_threshold
Alcanivorax limicola	strain=JB21	GCA_019931215.1	2874102	2874102	type	True	77.6993	223	1355	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	76.3283	146	1355	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	76.3059	149	1355	95	below_threshold
Thioalkalivibrio thiocyanodenitrificans	strain=ARhD 1	GCA_000378965.1	243063	243063	type	True	75.4322	82	1355	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:03:50,152] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36616/tc_result.tsv
[2023-03-18 23:03:50,152] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:03:50,152] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:03:50,152] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab3bd6ce-a5b9-42b4-8c00-26f73b3fe0eb/dqc_reference/checkm_data
[2023-03-18 23:03:50,153] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:03:50,159] [INFO] Task started: CheckM
[2023-03-18 23:03:50,159] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36616/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36616/checkm_input OceanDNA-b36616/checkm_result
[2023-03-18 23:04:53,470] [INFO] Task succeeded: CheckM
[2023-03-18 23:04:53,470] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:04:53,473] [INFO] ===== Completeness check finished =====
[2023-03-18 23:04:53,473] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:04:53,473] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36616/markers.fasta)
[2023-03-18 23:04:53,474] [INFO] Task started: Blastn
[2023-03-18 23:04:53,474] [INFO] Running command: blastn -query OceanDNA-b36616/markers.fasta -db /var/lib/cwl/stgab3bd6ce-a5b9-42b4-8c00-26f73b3fe0eb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36616/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:04:54,823] [INFO] Task succeeded: Blastn
[2023-03-18 23:04:54,824] [INFO] Selected 9 target genomes.
[2023-03-18 23:04:54,824] [INFO] Target genome list was writen to OceanDNA-b36616/target_genomes_gtdb.txt
[2023-03-18 23:04:54,835] [INFO] Task started: fastANI
[2023-03-18 23:04:54,836] [INFO] Running command: fastANI --query /var/lib/cwl/stg89f44a70-8a8d-4205-b60a-0eac49d3a285/OceanDNA-b36616.fa --refList OceanDNA-b36616/target_genomes_gtdb.txt --output OceanDNA-b36616/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:05:03,358] [INFO] Task succeeded: fastANI
[2023-03-18 23:05:03,364] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:05:03,364] [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
GCF_900217905.1	s__Alcanivorax xenomutans	98.3774	1239	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.43	98.18	0.92	0.84	9	conclusive
GCF_000300005.1	s__Alcanivorax dieselolei	93.6494	1220	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.56	95.12	0.92	0.84	3	-
GCF_004360225.1	s__Alcanivorax sp004360225	91.1756	1188	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	99.14	99.14	0.91	0.91	2	-
GCF_015265435.1	s__Alcanivorax profundimaris	80.3703	668	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.49	97.23	0.85	0.77	11	-
GCF_016906305.1	s__Alcanivorax marinus_B	80.3114	640	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016785095.1	s__Alcanivorax marinus_A	80.2668	623	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938655.1	s__Alcanivorax gelatiniphagus	80.221	652	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.53	98.53	0.93	0.93	3	-
GCA_017794945.1	s__Alcanivorax sp009711585	79.9519	530	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	96.99	96.99	0.93	0.93	2	-
GCA_003862375.1	s__Alcanivorax jadensis_A	78.7175	379	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	99.67	99.67	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-18 23:05:03,365] [INFO] GTDB search result was written to OceanDNA-b36616/result_gtdb.tsv
[2023-03-18 23:05:03,365] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:05:03,366] [INFO] DFAST_QC result json was written to OceanDNA-b36616/dqc_result.json
[2023-03-18 23:05:03,366] [INFO] DFAST_QC completed!
[2023-03-18 23:05:03,366] [INFO] Total running time: 0h1m49s