[2023-03-18 07:58:06,153] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:58:06,153] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:58:06,153] [INFO] DQC Reference Directory: /var/lib/cwl/stg245daf18-f94a-46a4-8e29-fcdb8e79de7f/dqc_reference
[2023-03-18 07:58:07,269] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:58:07,269] [INFO] Task started: Prodigal
[2023-03-18 07:58:07,269] [INFO] Running command: cat /var/lib/cwl/stg450c3346-895d-462e-b7d2-ae7c795b9f04/OceanDNA-b9760.fa | prodigal -d OceanDNA-b9760/cds.fna -a OceanDNA-b9760/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:58:30,433] [INFO] Task succeeded: Prodigal
[2023-03-18 07:58:30,433] [INFO] Task started: HMMsearch
[2023-03-18 07:58:30,433] [INFO] Running command: hmmsearch --tblout OceanDNA-b9760/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg245daf18-f94a-46a4-8e29-fcdb8e79de7f/dqc_reference/reference_markers.hmm OceanDNA-b9760/protein.faa > /dev/null
[2023-03-18 07:58:30,640] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:58:30,641] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg450c3346-895d-462e-b7d2-ae7c795b9f04/OceanDNA-b9760.fa]
[2023-03-18 07:58:30,660] [INFO] Query marker FASTA was written to OceanDNA-b9760/markers.fasta
[2023-03-18 07:58:30,660] [INFO] Task started: Blastn
[2023-03-18 07:58:30,660] [INFO] Running command: blastn -query OceanDNA-b9760/markers.fasta -db /var/lib/cwl/stg245daf18-f94a-46a4-8e29-fcdb8e79de7f/dqc_reference/reference_markers.fasta -out OceanDNA-b9760/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:58:31,233] [INFO] Task succeeded: Blastn
[2023-03-18 07:58:31,234] [INFO] Selected 12 target genomes.
[2023-03-18 07:58:31,234] [INFO] Target genome list was writen to OceanDNA-b9760/target_genomes.txt
[2023-03-18 07:58:31,238] [INFO] Task started: fastANI
[2023-03-18 07:58:31,238] [INFO] Running command: fastANI --query /var/lib/cwl/stg450c3346-895d-462e-b7d2-ae7c795b9f04/OceanDNA-b9760.fa --refList OceanDNA-b9760/target_genomes.txt --output OceanDNA-b9760/fastani_result.tsv --threads 1
[2023-03-18 07:58:39,778] [INFO] Task succeeded: fastANI
[2023-03-18 07:58:39,778] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg245daf18-f94a-46a4-8e29-fcdb8e79de7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:58:39,778] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg245daf18-f94a-46a4-8e29-fcdb8e79de7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:58:39,785] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 07:58:39,786] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 07:58:39,786] [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
Muricauda lutimaris	strain=KCTC 22173	GCA_003581615.1	475082	475082	type	True	98.0753	860	951	95	conclusive
Muricauda ruestringensis	strain=DSM 13258	GCA_000224085.1	111501	111501	type	True	83.0853	652	951	95	below_threshold
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	82.3618	723	951	95	below_threshold
Muricauda oceani	strain=501str8	GCA_019457985.1	2698672	2698672	type	True	81.7235	589	951	95	below_threshold
Muricauda oceani	strain=501str8	GCA_011068285.1	2698672	2698672	type	True	81.7084	598	951	95	below_threshold
Muricauda oceanensis	strain=40DY170	GCA_003992595.1	2499163	2499163	type	True	81.4868	628	951	95	below_threshold
Muricauda aurea	strain=BC31-1-A7	GCA_017313785.1	2915619	2915619	type	True	81.1979	590	951	95	below_threshold
Muricauda brasiliensis	strain=K001	GCA_003057865.1	2162892	2162892	type	True	80.8892	579	951	95	below_threshold
Muricauda chongwuensis	strain=HICW	GCA_013376415.1	2697365	2697365	type	True	80.8612	587	951	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	78.1083	334	951	95	below_threshold
Muricauda hymeniacidonis	strain=176CP4-71	GCA_004296335.1	2517819	2517819	type	True	76.6279	145	951	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:58:39,786] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9760/tc_result.tsv
[2023-03-18 07:58:39,786] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:58:39,786] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:58:39,786] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg245daf18-f94a-46a4-8e29-fcdb8e79de7f/dqc_reference/checkm_data
[2023-03-18 07:58:39,787] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:58:39,791] [INFO] Task started: CheckM
[2023-03-18 07:58:39,791] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9760/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9760/checkm_input OceanDNA-b9760/checkm_result
[2023-03-18 07:59:38,240] [INFO] Task succeeded: CheckM
[2023-03-18 07:59:38,241] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:59:38,243] [INFO] ===== Completeness check finished =====
[2023-03-18 07:59:38,243] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:59:38,243] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9760/markers.fasta)
[2023-03-18 07:59:38,243] [INFO] Task started: Blastn
[2023-03-18 07:59:38,243] [INFO] Running command: blastn -query OceanDNA-b9760/markers.fasta -db /var/lib/cwl/stg245daf18-f94a-46a4-8e29-fcdb8e79de7f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9760/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:59:39,044] [INFO] Task succeeded: Blastn
[2023-03-18 07:59:39,044] [INFO] Selected 8 target genomes.
[2023-03-18 07:59:39,045] [INFO] Target genome list was writen to OceanDNA-b9760/target_genomes_gtdb.txt
[2023-03-18 07:59:39,052] [INFO] Task started: fastANI
[2023-03-18 07:59:39,052] [INFO] Running command: fastANI --query /var/lib/cwl/stg450c3346-895d-462e-b7d2-ae7c795b9f04/OceanDNA-b9760.fa --refList OceanDNA-b9760/target_genomes_gtdb.txt --output OceanDNA-b9760/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:59:45,755] [INFO] Task succeeded: fastANI
[2023-03-18 07:59:45,761] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 07:59:45,761] [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
GCF_003581615.1	s__Muricauda lutimaris	98.0753	860	951	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002167435.2	s__Muricauda sp002167435	88.9525	758	951	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813125.1	s__Muricauda sp002813125	88.5036	781	951	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000224085.1	s__Muricauda ruestringensis	83.0822	652	951	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911645.1	s__Muricauda sp013911645	82.7365	641	951	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313105.1	s__Muricauda sp017313105	82.3831	696	951	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010468565.1	s__Muricauda sp010468565	82.2926	634	951	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699205.1	s__Muricauda sp002699205	81.6043	595	951	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.91	99.91	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-03-18 07:59:45,761] [INFO] GTDB search result was written to OceanDNA-b9760/result_gtdb.tsv
[2023-03-18 07:59:45,761] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:59:45,762] [INFO] DFAST_QC result json was written to OceanDNA-b9760/dqc_result.json
[2023-03-18 07:59:45,762] [INFO] DFAST_QC completed!
[2023-03-18 07:59:45,762] [INFO] Total running time: 0h1m40s