[2023-03-16 10:35:47,814] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:35:47,814] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:35:47,814] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f8d599b-fa66-48d5-bf8f-9470cd2d0f7e/dqc_reference
[2023-03-16 10:35:48,981] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:35:48,982] [INFO] Task started: Prodigal
[2023-03-16 10:35:48,983] [INFO] Running command: cat /var/lib/cwl/stg2a26ff50-a956-47cc-a1d1-018625b2eec6/OceanDNA-b23584.fa | prodigal -d OceanDNA-b23584/cds.fna -a OceanDNA-b23584/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:36:11,064] [INFO] Task succeeded: Prodigal
[2023-03-16 10:36:11,064] [INFO] Task started: HMMsearch
[2023-03-16 10:36:11,064] [INFO] Running command: hmmsearch --tblout OceanDNA-b23584/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f8d599b-fa66-48d5-bf8f-9470cd2d0f7e/dqc_reference/reference_markers.hmm OceanDNA-b23584/protein.faa > /dev/null
[2023-03-16 10:36:11,317] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:36:11,318] [INFO] Found 6/6 markers.
[2023-03-16 10:36:11,342] [INFO] Query marker FASTA was written to OceanDNA-b23584/markers.fasta
[2023-03-16 10:36:11,343] [INFO] Task started: Blastn
[2023-03-16 10:36:11,343] [INFO] Running command: blastn -query OceanDNA-b23584/markers.fasta -db /var/lib/cwl/stg1f8d599b-fa66-48d5-bf8f-9470cd2d0f7e/dqc_reference/reference_markers.fasta -out OceanDNA-b23584/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:36:12,286] [INFO] Task succeeded: Blastn
[2023-03-16 10:36:12,287] [INFO] Selected 12 target genomes.
[2023-03-16 10:36:12,287] [INFO] Target genome list was writen to OceanDNA-b23584/target_genomes.txt
[2023-03-16 10:36:12,294] [INFO] Task started: fastANI
[2023-03-16 10:36:12,294] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a26ff50-a956-47cc-a1d1-018625b2eec6/OceanDNA-b23584.fa --refList OceanDNA-b23584/target_genomes.txt --output OceanDNA-b23584/fastani_result.tsv --threads 1
[2023-03-16 10:36:22,058] [INFO] Task succeeded: fastANI
[2023-03-16 10:36:22,059] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f8d599b-fa66-48d5-bf8f-9470cd2d0f7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:36:22,059] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f8d599b-fa66-48d5-bf8f-9470cd2d0f7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:36:22,067] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:36:22,067] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 10:36:22,067] [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
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	83.1771	790	1115	95	below_threshold
Hyphomonas oceanitis	strain=SCH89	GCA_000685295.1	81033	81033	type	True	83.0577	794	1115	95	below_threshold
Hyphomonas johnsonii	strain=MHS-2	GCA_000685275.1	81031	81031	type	True	82.6384	748	1115	95	below_threshold
Hyphomonas jannaschiana	strain=VP2	GCA_000685215.1	86	86	type	True	78.844	482	1115	95	below_threshold
Hyphomonas adhaerens	strain=MHS-3	GCA_000685235.1	81029	81029	type	True	78.7095	473	1115	95	below_threshold
Hyphomonas sediminis	strain=WL0036	GCA_019679475.1	2866160	2866160	type	True	78.0951	362	1115	95	below_threshold
Hyphomonas atlantica	strain=22II1-22F38	GCA_000682715.1	1280948	1280948	type	True	77.9004	332	1115	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	77.4668	291	1115	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	76.0595	98	1115	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	76.0317	94	1115	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	75.8328	103	1115	95	below_threshold
Methylobacterium tardum	strain=DSM 19566	GCA_023546765.1	374432	374432	type	True	75.5612	90	1115	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 10:36:22,067] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23584/tc_result.tsv
[2023-03-16 10:36:22,068] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:36:22,068] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:36:22,068] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f8d599b-fa66-48d5-bf8f-9470cd2d0f7e/dqc_reference/checkm_data
[2023-03-16 10:36:22,069] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:36:22,073] [INFO] Task started: CheckM
[2023-03-16 10:36:22,074] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23584/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23584/checkm_input OceanDNA-b23584/checkm_result
[2023-03-16 10:37:19,058] [INFO] Task succeeded: CheckM
[2023-03-16 10:37:19,059] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:37:19,062] [INFO] ===== Completeness check finished =====
[2023-03-16 10:37:19,062] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:37:19,062] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23584/markers.fasta)
[2023-03-16 10:37:19,063] [INFO] Task started: Blastn
[2023-03-16 10:37:19,063] [INFO] Running command: blastn -query OceanDNA-b23584/markers.fasta -db /var/lib/cwl/stg1f8d599b-fa66-48d5-bf8f-9470cd2d0f7e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23584/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:37:20,913] [INFO] Task succeeded: Blastn
[2023-03-16 10:37:20,914] [INFO] Selected 7 target genomes.
[2023-03-16 10:37:20,914] [INFO] Target genome list was writen to OceanDNA-b23584/target_genomes_gtdb.txt
[2023-03-16 10:37:20,924] [INFO] Task started: fastANI
[2023-03-16 10:37:20,924] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a26ff50-a956-47cc-a1d1-018625b2eec6/OceanDNA-b23584.fa --refList OceanDNA-b23584/target_genomes_gtdb.txt --output OceanDNA-b23584/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:37:26,880] [INFO] Task succeeded: fastANI
[2023-03-16 10:37:26,885] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:37:26,885] [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_018830285.1	s__Hyphomonas sp018830285	89.9769	923	1115	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961795.1	s__Hyphomonas sp000961795	83.5448	753	1115	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000682695.1	s__Hyphomonas chukchiensis	83.1771	790	1115	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685295.1	s__Hyphomonas oceanitis	83.0475	794	1115	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685275.1	s__Hyphomonas johnsonii	82.6384	748	1115	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018827375.1	s__Hyphomonas sp018827375	82.076	730	1115	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.92	99.88	0.98	0.97	4	-
--------------------------------------------------------------------------------
[2023-03-16 10:37:26,885] [INFO] GTDB search result was written to OceanDNA-b23584/result_gtdb.tsv
[2023-03-16 10:37:26,886] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:37:26,887] [INFO] DFAST_QC result json was written to OceanDNA-b23584/dqc_result.json
[2023-03-16 10:37:26,887] [INFO] DFAST_QC completed!
[2023-03-16 10:37:26,887] [INFO] Total running time: 0h1m39s