[2023-03-17 09:41:39,968] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:41:39,970] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:41:39,970] [INFO] DQC Reference Directory: /var/lib/cwl/stg2593f538-2fc8-411e-ba89-0f17777b9268/dqc_reference
[2023-03-17 09:41:41,755] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:41:41,756] [INFO] Task started: Prodigal
[2023-03-17 09:41:41,756] [INFO] Running command: cat /var/lib/cwl/stg6f989971-34a8-41d7-957e-dc0640f0796d/OceanDNA-b6493.fa | prodigal -d OceanDNA-b6493/cds.fna -a OceanDNA-b6493/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:42:01,493] [INFO] Task succeeded: Prodigal
[2023-03-17 09:42:01,494] [INFO] Task started: HMMsearch
[2023-03-17 09:42:01,494] [INFO] Running command: hmmsearch --tblout OceanDNA-b6493/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2593f538-2fc8-411e-ba89-0f17777b9268/dqc_reference/reference_markers.hmm OceanDNA-b6493/protein.faa > /dev/null
[2023-03-17 09:42:01,702] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:42:01,702] [INFO] Found 6/6 markers.
[2023-03-17 09:42:01,728] [INFO] Query marker FASTA was written to OceanDNA-b6493/markers.fasta
[2023-03-17 09:42:01,731] [INFO] Task started: Blastn
[2023-03-17 09:42:01,731] [INFO] Running command: blastn -query OceanDNA-b6493/markers.fasta -db /var/lib/cwl/stg2593f538-2fc8-411e-ba89-0f17777b9268/dqc_reference/reference_markers.fasta -out OceanDNA-b6493/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:42:02,335] [INFO] Task succeeded: Blastn
[2023-03-17 09:42:02,345] [INFO] Selected 15 target genomes.
[2023-03-17 09:42:02,345] [INFO] Target genome list was writen to OceanDNA-b6493/target_genomes.txt
[2023-03-17 09:42:02,460] [INFO] Task started: fastANI
[2023-03-17 09:42:02,460] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f989971-34a8-41d7-957e-dc0640f0796d/OceanDNA-b6493.fa --refList OceanDNA-b6493/target_genomes.txt --output OceanDNA-b6493/fastani_result.tsv --threads 1
[2023-03-17 09:42:13,273] [INFO] Task succeeded: fastANI
[2023-03-17 09:42:13,274] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2593f538-2fc8-411e-ba89-0f17777b9268/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:42:13,274] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2593f538-2fc8-411e-ba89-0f17777b9268/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:42:13,284] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:42:13,284] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 09:42:13,284] [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
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	81.342	587	1004	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	80.3122	490	1004	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	80.237	497	1004	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	80.2304	498	1004	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	80.1328	539	1004	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	80.1137	537	1004	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	79.965	481	1004	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	78.5914	341	1004	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	78.5492	439	1004	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	78.3987	372	1004	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	78.3724	363	1004	95	below_threshold
Flavivirga eckloniae	strain=ECD14	GCA_002886045.1	1803846	1803846	type	True	78.3429	363	1004	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.6002	290	1004	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	77.1749	232	1004	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	76.8017	206	1004	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 09:42:13,286] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6493/tc_result.tsv
[2023-03-17 09:42:13,289] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:42:13,289] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:42:13,290] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2593f538-2fc8-411e-ba89-0f17777b9268/dqc_reference/checkm_data
[2023-03-17 09:42:13,290] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:42:13,344] [INFO] Task started: CheckM
[2023-03-17 09:42:13,345] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6493/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6493/checkm_input OceanDNA-b6493/checkm_result
[2023-03-17 09:43:04,274] [INFO] Task succeeded: CheckM
[2023-03-17 09:43:04,275] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:43:04,309] [INFO] ===== Completeness check finished =====
[2023-03-17 09:43:04,310] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:43:04,310] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6493/markers.fasta)
[2023-03-17 09:43:04,312] [INFO] Task started: Blastn
[2023-03-17 09:43:04,312] [INFO] Running command: blastn -query OceanDNA-b6493/markers.fasta -db /var/lib/cwl/stg2593f538-2fc8-411e-ba89-0f17777b9268/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6493/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:43:05,201] [INFO] Task succeeded: Blastn
[2023-03-17 09:43:05,219] [INFO] Selected 14 target genomes.
[2023-03-17 09:43:05,219] [INFO] Target genome list was writen to OceanDNA-b6493/target_genomes_gtdb.txt
[2023-03-17 09:43:05,456] [INFO] Task started: fastANI
[2023-03-17 09:43:05,456] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f989971-34a8-41d7-957e-dc0640f0796d/OceanDNA-b6493.fa --refList OceanDNA-b6493/target_genomes_gtdb.txt --output OceanDNA-b6493/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:43:15,896] [INFO] Task succeeded: fastANI
[2023-03-17 09:43:15,904] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 09:43:15,905] [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_905480415.1	s__Algibacter_B sp905480415	86.8292	590	1004	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	81.3306	588	1004	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202225.1	s__Algibacter_B amylolyticus	80.3134	491	1004	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	100.00	100.00	1.00	1.00	3	-
GCF_900141715.1	s__Arenitalea lutea	80.1222	540	1004	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900112595.1	s__Algibacter_B pectinivorans	79.9361	484	1004	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	79.8894	506	1004	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789235.1	s__Wocania ichthyoenteri	79.7183	488	1004	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001275.1	s__Flaviramulus sp013001275	79.4907	386	1004	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741945.1	s__Wocania sp002741945	79.0165	425	1004	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747085.1	s__Algibacter_C aquaticus	78.9834	427	1004	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796825.1	s__Algibacter sp009796825	78.6416	378	1004	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791695.1	s__Flavivirga rizhaonensis	78.5491	439	1004	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008056315.1	s__Seonamhaeicola maritimus	78.3724	363	1004	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310335.1	s__Jejuia pacifica	77.8008	343	1004	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-17 09:43:15,908] [INFO] GTDB search result was written to OceanDNA-b6493/result_gtdb.tsv
[2023-03-17 09:43:15,911] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:43:15,917] [INFO] DFAST_QC result json was written to OceanDNA-b6493/dqc_result.json
[2023-03-17 09:43:15,917] [INFO] DFAST_QC completed!
[2023-03-17 09:43:15,918] [INFO] Total running time: 0h1m36s