[2023-03-17 05:10:04,752] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:10:04,752] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:10:04,752] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ec039e1-2f97-4161-95f1-8a99435737c1/dqc_reference
[2023-03-17 05:10:05,937] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:10:05,937] [INFO] Task started: Prodigal
[2023-03-17 05:10:05,937] [INFO] Running command: cat /var/lib/cwl/stgc5e0667a-acfb-4fcf-8e38-eb43c7b73e54/OceanDNA-b23814.fa | prodigal -d OceanDNA-b23814/cds.fna -a OceanDNA-b23814/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:10:26,120] [INFO] Task succeeded: Prodigal
[2023-03-17 05:10:26,121] [INFO] Task started: HMMsearch
[2023-03-17 05:10:26,121] [INFO] Running command: hmmsearch --tblout OceanDNA-b23814/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ec039e1-2f97-4161-95f1-8a99435737c1/dqc_reference/reference_markers.hmm OceanDNA-b23814/protein.faa > /dev/null
[2023-03-17 05:10:26,331] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:10:26,331] [INFO] Found 6/6 markers.
[2023-03-17 05:10:26,351] [INFO] Query marker FASTA was written to OceanDNA-b23814/markers.fasta
[2023-03-17 05:10:26,352] [INFO] Task started: Blastn
[2023-03-17 05:10:26,352] [INFO] Running command: blastn -query OceanDNA-b23814/markers.fasta -db /var/lib/cwl/stg1ec039e1-2f97-4161-95f1-8a99435737c1/dqc_reference/reference_markers.fasta -out OceanDNA-b23814/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:10:26,951] [INFO] Task succeeded: Blastn
[2023-03-17 05:10:26,952] [INFO] Selected 26 target genomes.
[2023-03-17 05:10:26,952] [INFO] Target genome list was writen to OceanDNA-b23814/target_genomes.txt
[2023-03-17 05:10:26,970] [INFO] Task started: fastANI
[2023-03-17 05:10:26,970] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5e0667a-acfb-4fcf-8e38-eb43c7b73e54/OceanDNA-b23814.fa --refList OceanDNA-b23814/target_genomes.txt --output OceanDNA-b23814/fastani_result.tsv --threads 1
[2023-03-17 05:10:42,732] [INFO] Task succeeded: fastANI
[2023-03-17 05:10:42,732] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ec039e1-2f97-4161-95f1-8a99435737c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:10:42,732] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ec039e1-2f97-4161-95f1-8a99435737c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:10:42,740] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:10:42,741] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 05:10:42,741] [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
Ponticaulis koreensis	strain=DSM 19734	GCA_000420665.1	1123045	1123045	type	True	79.7379	448	1098	95	below_threshold
Henriciella litoralis	strain=DSM 22014	GCA_002088935.1	568102	568102	type	True	76.3482	76	1098	95	below_threshold
Hyphomonas beringensis	strain=25B14_1	GCA_000682755.1	1280946	1280946	type	True	76.3316	63	1098	95	below_threshold
Henriciella algicola	strain=CCUG67844	GCA_003576245.1	1608422	1608422	type	True	76.1439	79	1098	95	below_threshold
Hyphomonas oceanitis	strain=SCH89	GCA_000685295.1	81033	81033	type	True	76.0986	51	1098	95	below_threshold
Henriciella pelagia	strain=LA220	GCA_002088945.1	1977912	1977912	type	True	75.9744	50	1098	95	below_threshold
Hyphomonas adhaerens	strain=MHS-3	GCA_000685235.1	81029	81029	type	True	75.9733	58	1098	95	below_threshold
Henriciella pelagia	strain=CGMCC 1.15928	GCA_014644035.1	1977912	1977912	type	True	75.9469	51	1098	95	below_threshold
Hyphomonas pacifica	strain=T16B2	GCA_000682675.1	1280941	1280941	type	True	75.8595	74	1098	95	below_threshold
Henriciella marina	strain=DSM 19595	GCA_000376805.1	453851	453851	type	True	75.8453	53	1098	95	below_threshold
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	75.6614	52	1098	95	below_threshold
Hyphomonas sediminis	strain=WL0036	GCA_019679475.1	2866160	2866160	type	True	75.6286	57	1098	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:10:42,741] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23814/tc_result.tsv
[2023-03-17 05:10:42,741] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:10:42,741] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:10:42,741] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ec039e1-2f97-4161-95f1-8a99435737c1/dqc_reference/checkm_data
[2023-03-17 05:10:42,742] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:10:42,747] [INFO] Task started: CheckM
[2023-03-17 05:10:42,747] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23814/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23814/checkm_input OceanDNA-b23814/checkm_result
[2023-03-17 05:11:36,967] [INFO] Task succeeded: CheckM
[2023-03-17 05:11:36,967] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.91%
Contamintation: 25.38%
Strain heterogeneity: 57.14%
--------------------------------------------------------------------------------
[2023-03-17 05:11:36,970] [INFO] ===== Completeness check finished =====
[2023-03-17 05:11:36,970] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:11:36,970] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23814/markers.fasta)
[2023-03-17 05:11:36,972] [INFO] Task started: Blastn
[2023-03-17 05:11:36,972] [INFO] Running command: blastn -query OceanDNA-b23814/markers.fasta -db /var/lib/cwl/stg1ec039e1-2f97-4161-95f1-8a99435737c1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23814/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:11:37,844] [INFO] Task succeeded: Blastn
[2023-03-17 05:11:37,845] [INFO] Selected 13 target genomes.
[2023-03-17 05:11:37,845] [INFO] Target genome list was writen to OceanDNA-b23814/target_genomes_gtdb.txt
[2023-03-17 05:11:38,081] [INFO] Task started: fastANI
[2023-03-17 05:11:38,081] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5e0667a-acfb-4fcf-8e38-eb43c7b73e54/OceanDNA-b23814.fa --refList OceanDNA-b23814/target_genomes_gtdb.txt --output OceanDNA-b23814/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:11:46,647] [INFO] Task succeeded: fastANI
[2023-03-17 05:11:46,655] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:11:46,655] [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_002173095.1	s__Ponticaulis sp002173095	99.9468	1034	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Ponticaulis	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_002338565.1	s__Ponticaulis sp002338565	80.7202	506	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Ponticaulis	95.0	99.94	99.86	0.98	0.96	4	-
GCA_002723155.1	s__Ponticaulis sp002723155	80.1363	490	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Ponticaulis	95.0	99.28	99.28	0.86	0.86	2	-
GCF_000420665.1	s__Ponticaulis koreensis	79.7264	449	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Ponticaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701295.1	s__Ponticaulis sp002701295	77.9247	229	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Ponticaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002692725.1	s__Ponticaulis sp002692725	77.553	269	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Ponticaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699325.1	s__Ponticaulis sp002699325	77.2748	210	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Ponticaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685295.1	s__Hyphomonas oceanitis	76.0986	51	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222605.1	s__Hyphomonas sp002695785	76.0852	76	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.58	99.58	0.85	0.85	2	-
GCF_000685235.1	s__Hyphomonas adhaerens	75.9979	57	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	97.03	96.92	0.83	0.82	4	-
GCF_002088945.1	s__Henriciella pelagia	75.9744	50	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000682675.1	s__Hyphomonas pacifica	75.8595	74	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.59	99.19	0.95	0.91	3	-
GCF_000682695.1	s__Hyphomonas chukchiensis	75.6614	52	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:11:46,655] [INFO] GTDB search result was written to OceanDNA-b23814/result_gtdb.tsv
[2023-03-17 05:11:46,655] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:11:46,657] [INFO] DFAST_QC result json was written to OceanDNA-b23814/dqc_result.json
[2023-03-17 05:11:46,657] [INFO] DFAST_QC completed!
[2023-03-17 05:11:46,657] [INFO] Total running time: 0h1m42s