[2023-03-18 20:55:47,234] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:55:47,234] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:55:47,234] [INFO] DQC Reference Directory: /var/lib/cwl/stgaffe2b96-483f-4a04-bfd8-a940e2a7c34d/dqc_reference
[2023-03-18 20:55:48,399] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:55:48,399] [INFO] Task started: Prodigal
[2023-03-18 20:55:48,400] [INFO] Running command: cat /var/lib/cwl/stgc29eaaec-4425-4d0d-b1c5-f3bfefdfd332/OceanDNA-b2345.fa | prodigal -d OceanDNA-b2345/cds.fna -a OceanDNA-b2345/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:55:52,512] [INFO] Task succeeded: Prodigal
[2023-03-18 20:55:52,512] [INFO] Task started: HMMsearch
[2023-03-18 20:55:52,512] [INFO] Running command: hmmsearch --tblout OceanDNA-b2345/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaffe2b96-483f-4a04-bfd8-a940e2a7c34d/dqc_reference/reference_markers.hmm OceanDNA-b2345/protein.faa > /dev/null
[2023-03-18 20:55:52,665] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:55:52,665] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc29eaaec-4425-4d0d-b1c5-f3bfefdfd332/OceanDNA-b2345.fa]
[2023-03-18 20:55:52,672] [INFO] Query marker FASTA was written to OceanDNA-b2345/markers.fasta
[2023-03-18 20:55:52,674] [INFO] Task started: Blastn
[2023-03-18 20:55:52,674] [INFO] Running command: blastn -query OceanDNA-b2345/markers.fasta -db /var/lib/cwl/stgaffe2b96-483f-4a04-bfd8-a940e2a7c34d/dqc_reference/reference_markers.fasta -out OceanDNA-b2345/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:55:53,353] [INFO] Task succeeded: Blastn
[2023-03-18 20:55:53,354] [INFO] Selected 9 target genomes.
[2023-03-18 20:55:53,354] [INFO] Target genome list was writen to OceanDNA-b2345/target_genomes.txt
[2023-03-18 20:55:53,359] [INFO] Task started: fastANI
[2023-03-18 20:55:53,359] [INFO] Running command: fastANI --query /var/lib/cwl/stgc29eaaec-4425-4d0d-b1c5-f3bfefdfd332/OceanDNA-b2345.fa --refList OceanDNA-b2345/target_genomes.txt --output OceanDNA-b2345/fastani_result.tsv --threads 1
[2023-03-18 20:55:57,581] [INFO] Task succeeded: fastANI
[2023-03-18 20:55:57,581] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaffe2b96-483f-4a04-bfd8-a940e2a7c34d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:55:57,582] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaffe2b96-483f-4a04-bfd8-a940e2a7c34d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:55:57,582] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:55:57,582] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 20:55:57,582] [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 20:55:57,582] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2345/tc_result.tsv
[2023-03-18 20:55:57,582] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:55:57,582] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:55:57,582] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaffe2b96-483f-4a04-bfd8-a940e2a7c34d/dqc_reference/checkm_data
[2023-03-18 20:55:57,585] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:55:57,587] [INFO] Task started: CheckM
[2023-03-18 20:55:57,587] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2345/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2345/checkm_input OceanDNA-b2345/checkm_result
[2023-03-18 20:56:18,093] [INFO] Task succeeded: CheckM
[2023-03-18 20:56:18,093] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:56:18,094] [INFO] ===== Completeness check finished =====
[2023-03-18 20:56:18,095] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:56:18,095] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2345/markers.fasta)
[2023-03-18 20:56:18,096] [INFO] Task started: Blastn
[2023-03-18 20:56:18,097] [INFO] Running command: blastn -query OceanDNA-b2345/markers.fasta -db /var/lib/cwl/stgaffe2b96-483f-4a04-bfd8-a940e2a7c34d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2345/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:56:18,898] [INFO] Task succeeded: Blastn
[2023-03-18 20:56:18,899] [INFO] Selected 13 target genomes.
[2023-03-18 20:56:18,899] [INFO] Target genome list was writen to OceanDNA-b2345/target_genomes_gtdb.txt
[2023-03-18 20:56:19,088] [INFO] Task started: fastANI
[2023-03-18 20:56:19,088] [INFO] Running command: fastANI --query /var/lib/cwl/stgc29eaaec-4425-4d0d-b1c5-f3bfefdfd332/OceanDNA-b2345.fa --refList OceanDNA-b2345/target_genomes_gtdb.txt --output OceanDNA-b2345/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:56:21,137] [INFO] Task succeeded: fastANI
[2023-03-18 20:56:21,143] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 20:56:21,143] [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_002169115.2	s__Actinomarina sp002169115	95.1996	97	268	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	96.47	96.47	0.52	0.52	2	conclusive
GCA_902510965.1	s__Actinomarina sp002683085	94.955	174	268	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	93.6837	233	268	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	81.7753	183	268	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	80.6323	118	268	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902622665.1	s__Actinomarina sp902622665	77.9789	59	268	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902628045.1	s__Actinomarina sp902628045	77.9467	53	268	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016777845.1	s__Actinomarina sp016777845	77.5204	55	268	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003282445.1	s__Actinomarina sp003282445	77.4815	88	268	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 20:56:21,144] [INFO] GTDB search result was written to OceanDNA-b2345/result_gtdb.tsv
[2023-03-18 20:56:21,144] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:56:21,144] [INFO] DFAST_QC result json was written to OceanDNA-b2345/dqc_result.json
[2023-03-18 20:56:21,145] [INFO] DFAST_QC completed!
[2023-03-18 20:56:21,145] [INFO] Total running time: 0h0m34s