[2023-03-18 22:44:58,018] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:44:58,021] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:44:58,021] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe4ee51e-e5a5-406b-9e9e-70330b61e650/dqc_reference
[2023-03-18 22:44:59,111] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:44:59,111] [INFO] Task started: Prodigal
[2023-03-18 22:44:59,111] [INFO] Running command: cat /var/lib/cwl/stg06a469e4-277c-41cc-ad35-884a8822f599/OceanDNA-b2118.fa | prodigal -d OceanDNA-b2118/cds.fna -a OceanDNA-b2118/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:45:02,812] [INFO] Task succeeded: Prodigal
[2023-03-18 22:45:02,812] [INFO] Task started: HMMsearch
[2023-03-18 22:45:02,812] [INFO] Running command: hmmsearch --tblout OceanDNA-b2118/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe4ee51e-e5a5-406b-9e9e-70330b61e650/dqc_reference/reference_markers.hmm OceanDNA-b2118/protein.faa > /dev/null
[2023-03-18 22:45:02,973] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:45:02,974] [INFO] Found 6/6 markers.
[2023-03-18 22:45:03,002] [INFO] Query marker FASTA was written to OceanDNA-b2118/markers.fasta
[2023-03-18 22:45:03,002] [INFO] Task started: Blastn
[2023-03-18 22:45:03,002] [INFO] Running command: blastn -query OceanDNA-b2118/markers.fasta -db /var/lib/cwl/stgfe4ee51e-e5a5-406b-9e9e-70330b61e650/dqc_reference/reference_markers.fasta -out OceanDNA-b2118/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:45:03,499] [INFO] Task succeeded: Blastn
[2023-03-18 22:45:03,505] [INFO] Selected 16 target genomes.
[2023-03-18 22:45:03,505] [INFO] Target genome list was writen to OceanDNA-b2118/target_genomes.txt
[2023-03-18 22:45:03,516] [INFO] Task started: fastANI
[2023-03-18 22:45:03,516] [INFO] Running command: fastANI --query /var/lib/cwl/stg06a469e4-277c-41cc-ad35-884a8822f599/OceanDNA-b2118.fa --refList OceanDNA-b2118/target_genomes.txt --output OceanDNA-b2118/fastani_result.tsv --threads 1
[2023-03-18 22:45:09,985] [INFO] Task succeeded: fastANI
[2023-03-18 22:45:09,985] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe4ee51e-e5a5-406b-9e9e-70330b61e650/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:45:09,986] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe4ee51e-e5a5-406b-9e9e-70330b61e650/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:45:09,986] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:45:09,986] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:45:09,986] [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 22:45:09,987] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2118/tc_result.tsv
[2023-03-18 22:45:09,989] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:45:09,989] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:45:09,989] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe4ee51e-e5a5-406b-9e9e-70330b61e650/dqc_reference/checkm_data
[2023-03-18 22:45:09,992] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:45:09,996] [INFO] Task started: CheckM
[2023-03-18 22:45:09,996] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2118/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2118/checkm_input OceanDNA-b2118/checkm_result
[2023-03-18 22:45:25,887] [INFO] Task succeeded: CheckM
[2023-03-18 22:45:25,888] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.84%
Contamintation: 1.30%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-18 22:45:25,957] [INFO] ===== Completeness check finished =====
[2023-03-18 22:45:25,957] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:45:25,957] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2118/markers.fasta)
[2023-03-18 22:45:25,958] [INFO] Task started: Blastn
[2023-03-18 22:45:25,958] [INFO] Running command: blastn -query OceanDNA-b2118/markers.fasta -db /var/lib/cwl/stgfe4ee51e-e5a5-406b-9e9e-70330b61e650/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2118/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:45:26,702] [INFO] Task succeeded: Blastn
[2023-03-18 22:45:26,720] [INFO] Selected 14 target genomes.
[2023-03-18 22:45:26,720] [INFO] Target genome list was writen to OceanDNA-b2118/target_genomes_gtdb.txt
[2023-03-18 22:45:26,802] [INFO] Task started: fastANI
[2023-03-18 22:45:26,802] [INFO] Running command: fastANI --query /var/lib/cwl/stg06a469e4-277c-41cc-ad35-884a8822f599/OceanDNA-b2118.fa --refList OceanDNA-b2118/target_genomes_gtdb.txt --output OceanDNA-b2118/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:45:29,505] [INFO] Task succeeded: fastANI
[2023-03-18 22:45:29,510] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 22:45:29,510] [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_902510965.1	s__Actinomarina sp002683085	81.9153	128	238	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	98.49	98.44	0.76	0.76	3	-
GCA_014239265.1	s__Actinomarina sp014239265	81.8386	161	238	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002169845.1	s__Actinomarina sp002169845	81.6192	86	238	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014384285.1	s__Actinomarina sp014384285	80.1823	148	238	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	99.05	98.78	0.90	0.82	4	-
GCA_002308095.1	s__Actinomarina sp002308095	79.2716	93	238	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902593795.1	s__Actinomarina sp902593795	77.1442	50	238	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.69	97.47	0.86	0.85	3	-
GCA_003282445.1	s__Actinomarina sp003282445	76.8203	64	238	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.01	96.02	0.90	0.85	11	-
--------------------------------------------------------------------------------
[2023-03-18 22:45:29,512] [INFO] GTDB search result was written to OceanDNA-b2118/result_gtdb.tsv
[2023-03-18 22:45:29,513] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:45:29,516] [INFO] DFAST_QC result json was written to OceanDNA-b2118/dqc_result.json
[2023-03-18 22:45:29,516] [INFO] DFAST_QC completed!
[2023-03-18 22:45:29,516] [INFO] Total running time: 0h0m31s