[2023-03-18 21:50:26,971] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:50:26,972] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:50:26,972] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1878bac-0bc8-4604-a371-50c0c255757a/dqc_reference
[2023-03-18 21:50:28,078] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:50:28,078] [INFO] Task started: Prodigal
[2023-03-18 21:50:28,078] [INFO] Running command: cat /var/lib/cwl/stgd80a8bbe-2afa-4b8a-8e00-4810ab052153/OceanDNA-b23811.fa | prodigal -d OceanDNA-b23811/cds.fna -a OceanDNA-b23811/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:50:43,763] [INFO] Task succeeded: Prodigal
[2023-03-18 21:50:43,764] [INFO] Task started: HMMsearch
[2023-03-18 21:50:43,764] [INFO] Running command: hmmsearch --tblout OceanDNA-b23811/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1878bac-0bc8-4604-a371-50c0c255757a/dqc_reference/reference_markers.hmm OceanDNA-b23811/protein.faa > /dev/null
[2023-03-18 21:50:43,959] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:50:43,960] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd80a8bbe-2afa-4b8a-8e00-4810ab052153/OceanDNA-b23811.fa]
[2023-03-18 21:50:43,975] [INFO] Query marker FASTA was written to OceanDNA-b23811/markers.fasta
[2023-03-18 21:50:43,976] [INFO] Task started: Blastn
[2023-03-18 21:50:43,976] [INFO] Running command: blastn -query OceanDNA-b23811/markers.fasta -db /var/lib/cwl/stgc1878bac-0bc8-4604-a371-50c0c255757a/dqc_reference/reference_markers.fasta -out OceanDNA-b23811/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:50:44,574] [INFO] Task succeeded: Blastn
[2023-03-18 21:50:44,851] [INFO] Selected 13 target genomes.
[2023-03-18 21:50:44,851] [INFO] Target genome list was writen to OceanDNA-b23811/target_genomes.txt
[2023-03-18 21:50:44,858] [INFO] Task started: fastANI
[2023-03-18 21:50:44,858] [INFO] Running command: fastANI --query /var/lib/cwl/stgd80a8bbe-2afa-4b8a-8e00-4810ab052153/OceanDNA-b23811.fa --refList OceanDNA-b23811/target_genomes.txt --output OceanDNA-b23811/fastani_result.tsv --threads 1
[2023-03-18 21:50:54,865] [INFO] Task succeeded: fastANI
[2023-03-18 21:50:54,865] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1878bac-0bc8-4604-a371-50c0c255757a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:50:54,865] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1878bac-0bc8-4604-a371-50c0c255757a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:50:54,872] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:50:54,872] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:50:54,872] [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 pacifica	strain=T16B2	GCA_000682675.1	1280941	1280941	type	True	92.5306	709	833	95	below_threshold
Hyphomonas beringensis	strain=25B14_1	GCA_000682755.1	1280946	1280946	type	True	89.5882	725	833	95	below_threshold
Hyphomonas atlantica	strain=22II1-22F38	GCA_000682715.1	1280948	1280948	type	True	80.111	444	833	95	below_threshold
Hyphomonas adhaerens	strain=MHS-3	GCA_000685235.1	81029	81029	type	True	79.2921	384	833	95	below_threshold
Hyphomonas jannaschiana	strain=VP2	GCA_000685215.1	86	86	type	True	79.2371	381	833	95	below_threshold
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	78.4807	340	833	95	below_threshold
Hyphomonas sediminis	strain=WL0036	GCA_019679475.1	2866160	2866160	type	True	77.8278	247	833	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	76.0514	61	833	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:50:54,873] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23811/tc_result.tsv
[2023-03-18 21:50:54,873] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:50:54,873] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:50:54,873] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1878bac-0bc8-4604-a371-50c0c255757a/dqc_reference/checkm_data
[2023-03-18 21:50:54,874] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:50:54,879] [INFO] Task started: CheckM
[2023-03-18 21:50:54,879] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23811/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23811/checkm_input OceanDNA-b23811/checkm_result
[2023-03-18 21:51:36,222] [INFO] Task succeeded: CheckM
[2023-03-18 21:51:36,223] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 21:51:36,225] [INFO] ===== Completeness check finished =====
[2023-03-18 21:51:36,225] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:51:36,225] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23811/markers.fasta)
[2023-03-18 21:51:36,226] [INFO] Task started: Blastn
[2023-03-18 21:51:36,226] [INFO] Running command: blastn -query OceanDNA-b23811/markers.fasta -db /var/lib/cwl/stgc1878bac-0bc8-4604-a371-50c0c255757a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23811/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:51:37,160] [INFO] Task succeeded: Blastn
[2023-03-18 21:51:37,161] [INFO] Selected 11 target genomes.
[2023-03-18 21:51:37,161] [INFO] Target genome list was writen to OceanDNA-b23811/target_genomes_gtdb.txt
[2023-03-18 21:51:37,170] [INFO] Task started: fastANI
[2023-03-18 21:51:37,170] [INFO] Running command: fastANI --query /var/lib/cwl/stgd80a8bbe-2afa-4b8a-8e00-4810ab052153/OceanDNA-b23811.fa --refList OceanDNA-b23811/target_genomes_gtdb.txt --output OceanDNA-b23811/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:51:44,226] [INFO] Task succeeded: fastANI
[2023-03-18 21:51:44,231] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 21:51:44,232] [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_018222605.1	s__Hyphomonas sp002695785	99.4928	812	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.58	99.58	0.85	0.85	2	conclusive
GCF_000682675.1	s__Hyphomonas pacifica	92.5083	710	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.59	99.19	0.95	0.91	3	-
GCF_000682755.1	s__Hyphomonas beringensis	89.5845	726	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792385.1	s__Hyphomonas sp017792385	80.4804	477	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002414505.1	s__Hyphomonas sp002414505	80.3979	417	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.04	98.84	0.81	0.74	4	-
GCF_000682715.1	s__Hyphomonas atlantica	80.111	444	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	98.47	98.11	0.91	0.87	6	-
GCF_000682775.1	s__Hyphomonas sp000682775	79.6713	440	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	95.72	95.47	0.88	0.83	38	-
GCF_000685235.1	s__Hyphomonas adhaerens	79.2921	384	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	97.03	96.92	0.83	0.82	4	-
--------------------------------------------------------------------------------
[2023-03-18 21:51:44,232] [INFO] GTDB search result was written to OceanDNA-b23811/result_gtdb.tsv
[2023-03-18 21:51:44,232] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:51:44,233] [INFO] DFAST_QC result json was written to OceanDNA-b23811/dqc_result.json
[2023-03-18 21:51:44,233] [INFO] DFAST_QC completed!
[2023-03-18 21:51:44,233] [INFO] Total running time: 0h1m17s