[2023-03-17 03:50:15,968] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:50:15,968] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:50:15,968] [INFO] DQC Reference Directory: /var/lib/cwl/stge3b9987b-4e6d-4334-9791-5809157cfc02/dqc_reference
[2023-03-17 03:50:17,139] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:50:17,139] [INFO] Task started: Prodigal
[2023-03-17 03:50:17,140] [INFO] Running command: cat /var/lib/cwl/stg445e6965-610f-45aa-8df8-4bf8c6edce7a/OceanDNA-b6838.fa | prodigal -d OceanDNA-b6838/cds.fna -a OceanDNA-b6838/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:50:34,226] [INFO] Task succeeded: Prodigal
[2023-03-17 03:50:34,226] [INFO] Task started: HMMsearch
[2023-03-17 03:50:34,226] [INFO] Running command: hmmsearch --tblout OceanDNA-b6838/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3b9987b-4e6d-4334-9791-5809157cfc02/dqc_reference/reference_markers.hmm OceanDNA-b6838/protein.faa > /dev/null
[2023-03-17 03:50:34,421] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:50:34,422] [INFO] Found 6/6 markers.
[2023-03-17 03:50:34,443] [INFO] Query marker FASTA was written to OceanDNA-b6838/markers.fasta
[2023-03-17 03:50:34,443] [INFO] Task started: Blastn
[2023-03-17 03:50:34,443] [INFO] Running command: blastn -query OceanDNA-b6838/markers.fasta -db /var/lib/cwl/stge3b9987b-4e6d-4334-9791-5809157cfc02/dqc_reference/reference_markers.fasta -out OceanDNA-b6838/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:50:35,019] [INFO] Task succeeded: Blastn
[2023-03-17 03:50:35,020] [INFO] Selected 14 target genomes.
[2023-03-17 03:50:35,020] [INFO] Target genome list was writen to OceanDNA-b6838/target_genomes.txt
[2023-03-17 03:50:35,027] [INFO] Task started: fastANI
[2023-03-17 03:50:35,027] [INFO] Running command: fastANI --query /var/lib/cwl/stg445e6965-610f-45aa-8df8-4bf8c6edce7a/OceanDNA-b6838.fa --refList OceanDNA-b6838/target_genomes.txt --output OceanDNA-b6838/fastani_result.tsv --threads 1
[2023-03-17 03:50:44,591] [INFO] Task succeeded: fastANI
[2023-03-17 03:50:44,591] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge3b9987b-4e6d-4334-9791-5809157cfc02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:50:44,591] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge3b9987b-4e6d-4334-9791-5809157cfc02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:50:44,599] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 03:50:44,599] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 03:50:44,599] [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
Flavobacterium beibuense	strain=F44-8	GCA_000769915.1	657326	657326	type	True	95.1181	792	860	95	conclusive
Flavobacterium rakeshii	strain=JCM 17928	GCA_009741375.1	1038845	1038845	type	True	92.2717	779	860	95	below_threshold
Flavobacterium alkalisoli	strain=XS-5	GCA_008000935.1	2602769	2602769	type	True	82.3127	649	860	95	below_threshold
Flavobacterium cerinum	strain=1E403	GCA_004028155.1	2502784	2502784	type	True	77.9839	262	860	95	below_threshold
Flavobacterium salilacus subsp. altitudinum	strain=LaA7.5	GCA_010078225.1	2691899	2898423	type	True	77.5396	232	860	95	below_threshold
Flavobacterium zepuense	strain=ZT4R6	GCA_007097145.1	2593302	2593302	type	True	77.4678	225	860	95	below_threshold
Flavobacterium litorale	strain=WSW3-B6	GCA_019613795.1	2856519	2856519	type	True	77.3489	177	860	95	below_threshold
Flavobacterium coralii	strain=D11R37	GCA_019891545.1	2838017	2838017	type	True	77.0637	191	860	95	below_threshold
Flavobacterium akiainvivens	strain=IK-1	GCA_001278115.1	1202724	1202724	type	True	76.7136	185	860	95	below_threshold
Flavobacterium akiainvivens	strain=DSM 25510	GCA_900115875.1	1202724	1202724	type	True	76.6982	187	860	95	below_threshold
Flavobacterium rhamnosiphilum	strain=LB3P52	GCA_004349195.1	2541724	2541724	type	True	76.2908	63	860	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 03:50:44,599] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6838/tc_result.tsv
[2023-03-17 03:50:44,599] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:50:44,599] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:50:44,599] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3b9987b-4e6d-4334-9791-5809157cfc02/dqc_reference/checkm_data
[2023-03-17 03:50:44,600] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:50:44,604] [INFO] Task started: CheckM
[2023-03-17 03:50:44,604] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6838/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6838/checkm_input OceanDNA-b6838/checkm_result
[2023-03-17 03:51:29,163] [INFO] Task succeeded: CheckM
[2023-03-17 03:51:29,163] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.88%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 03:51:29,165] [INFO] ===== Completeness check finished =====
[2023-03-17 03:51:29,165] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:51:29,166] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6838/markers.fasta)
[2023-03-17 03:51:29,166] [INFO] Task started: Blastn
[2023-03-17 03:51:29,166] [INFO] Running command: blastn -query OceanDNA-b6838/markers.fasta -db /var/lib/cwl/stge3b9987b-4e6d-4334-9791-5809157cfc02/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6838/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:51:29,932] [INFO] Task succeeded: Blastn
[2023-03-17 03:51:29,933] [INFO] Selected 9 target genomes.
[2023-03-17 03:51:29,933] [INFO] Target genome list was writen to OceanDNA-b6838/target_genomes_gtdb.txt
[2023-03-17 03:51:29,992] [INFO] Task started: fastANI
[2023-03-17 03:51:29,992] [INFO] Running command: fastANI --query /var/lib/cwl/stg445e6965-610f-45aa-8df8-4bf8c6edce7a/OceanDNA-b6838.fa --refList OceanDNA-b6838/target_genomes_gtdb.txt --output OceanDNA-b6838/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:51:36,661] [INFO] Task succeeded: fastANI
[2023-03-17 03:51:36,667] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 03:51:36,667] [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_000769915.1	s__Flavobacterium beibuense	95.1181	792	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009741375.1	s__Flavobacterium rakeshii	92.2717	779	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008000935.1	s__Flavobacterium alkalisoli	82.3215	648	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004151245.1	s__Flavobacterium beibuense_A	82.2788	621	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350375.1	s__Flavobacterium sp003350375	78.0981	288	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001708385.1	s__Flavobacterium psychrophilum_A	77.9632	268	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009848495.1	s__Flavobacterium sp009848495	77.4863	211	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344925.1	s__Flavobacterium arcticum	77.2724	226	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-17 03:51:36,667] [INFO] GTDB search result was written to OceanDNA-b6838/result_gtdb.tsv
[2023-03-17 03:51:36,667] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:51:36,669] [INFO] DFAST_QC result json was written to OceanDNA-b6838/dqc_result.json
[2023-03-17 03:51:36,669] [INFO] DFAST_QC completed!
[2023-03-17 03:51:36,669] [INFO] Total running time: 0h1m21s