[2023-03-19 05:19:33,749] [INFO] DFAST_QC pipeline started.
[2023-03-19 05:19:33,749] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 05:19:33,749] [INFO] DQC Reference Directory: /var/lib/cwl/stg72945ca1-c942-4d43-bf99-df7b78eded26/dqc_reference
[2023-03-19 05:19:35,407] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 05:19:35,407] [INFO] Task started: Prodigal
[2023-03-19 05:19:35,407] [INFO] Running command: cat /var/lib/cwl/stg574ee88f-095f-4187-987a-23e9dc0f0837/OceanDNA-b10728.fa | prodigal -d OceanDNA-b10728/cds.fna -a OceanDNA-b10728/protein.faa -g 11 -q > /dev/null
[2023-03-19 05:19:54,561] [INFO] Task succeeded: Prodigal
[2023-03-19 05:19:54,561] [INFO] Task started: HMMsearch
[2023-03-19 05:19:54,562] [INFO] Running command: hmmsearch --tblout OceanDNA-b10728/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72945ca1-c942-4d43-bf99-df7b78eded26/dqc_reference/reference_markers.hmm OceanDNA-b10728/protein.faa > /dev/null
[2023-03-19 05:19:54,834] [INFO] Task succeeded: HMMsearch
[2023-03-19 05:19:54,834] [INFO] Found 6/6 markers.
[2023-03-19 05:19:54,854] [INFO] Query marker FASTA was written to OceanDNA-b10728/markers.fasta
[2023-03-19 05:19:54,854] [INFO] Task started: Blastn
[2023-03-19 05:19:54,854] [INFO] Running command: blastn -query OceanDNA-b10728/markers.fasta -db /var/lib/cwl/stg72945ca1-c942-4d43-bf99-df7b78eded26/dqc_reference/reference_markers.fasta -out OceanDNA-b10728/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:19:55,454] [INFO] Task succeeded: Blastn
[2023-03-19 05:19:55,455] [INFO] Selected 24 target genomes.
[2023-03-19 05:19:55,455] [INFO] Target genome list was writen to OceanDNA-b10728/target_genomes.txt
[2023-03-19 05:19:55,465] [INFO] Task started: fastANI
[2023-03-19 05:19:55,465] [INFO] Running command: fastANI --query /var/lib/cwl/stg574ee88f-095f-4187-987a-23e9dc0f0837/OceanDNA-b10728.fa --refList OceanDNA-b10728/target_genomes.txt --output OceanDNA-b10728/fastani_result.tsv --threads 1
[2023-03-19 05:20:09,465] [INFO] Task succeeded: fastANI
[2023-03-19 05:20:09,465] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72945ca1-c942-4d43-bf99-df7b78eded26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 05:20:09,465] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72945ca1-c942-4d43-bf99-df7b78eded26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 05:20:09,477] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 05:20:09,477] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 05:20:09,477] [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
Marinirhabdus gelatinilytica	strain=DSM 101478	GCA_003353425.1	1703343	1703343	type	True	78.8955	356	920	95	below_threshold
Cochleicola gelatinilyticus	strain=LPB0005	GCA_001637325.1	1763537	1763537	type	True	77.1799	156	920	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	77.15	136	920	95	below_threshold
Winogradskyella schleiferi	strain=Z215	GCA_013394655.1	2686078	2686078	type	True	77.058	71	920	95	below_threshold
Marixanthomonas ophiurae	strain=KMM 3046	GCA_003413745.1	387659	387659	type	True	76.9674	162	920	95	below_threshold
Ulvibacter litoralis	strain=DSM 16195	GCA_900102055.1	227084	227084	type	True	76.9321	157	920	95	below_threshold
Constantimarinum furrinae	strain=ALE3EI	GCA_014295415.1	2562285	2562285	type	True	76.9281	121	920	95	below_threshold
Ulvibacter litoralis	strain=KCTC 12104	GCA_014651275.1	227084	227084	type	True	76.8997	162	920	95	below_threshold
Marixanthomonas spongiae	strain=HN-E44	GCA_003095375.1	2174845	2174845	type	True	76.8955	121	920	95	below_threshold
Hyunsoonleella pacifica	strain=SW033	GCA_004310335.1	1080224	1080224	type	True	76.7359	60	920	95	below_threshold
Hyunsoonleella pacifica	strain=CGMCC 1.11009	GCA_014636335.1	1080224	1080224	type	True	76.7359	60	920	95	below_threshold
Patiriisocius marinistellae	strain=KK4	GCA_009014635.1	2494560	2494560	type	True	76.7266	128	920	95	below_threshold
Aequorivita iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	76.7154	123	920	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.6858	63	920	95	below_threshold
Aequorivita soesokkakensis	strain=RSSK-12	GCA_001641085.1	1385699	1385699	type	True	76.6839	123	920	95	below_threshold
Ulvibacter antarcticus	strain=DSM 23424	GCA_003688405.1	442714	442714	type	True	76.6011	119	920	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	76.5747	61	920	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.405	64	920	95	below_threshold
Algibacter lectus	strain=DSM 15365	GCA_900112395.1	221126	221126	type	True	76.2085	60	920	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	76.182	61	920	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	76.1255	65	920	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 05:20:09,478] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10728/tc_result.tsv
[2023-03-19 05:20:09,478] [INFO] ===== Taxonomy check completed =====
[2023-03-19 05:20:09,478] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 05:20:09,478] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72945ca1-c942-4d43-bf99-df7b78eded26/dqc_reference/checkm_data
[2023-03-19 05:20:09,479] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 05:20:09,897] [INFO] Task started: CheckM
[2023-03-19 05:20:09,898] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10728/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10728/checkm_input OceanDNA-b10728/checkm_result
[2023-03-19 05:20:58,575] [INFO] Task succeeded: CheckM
[2023-03-19 05:20:58,575] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 05:20:58,578] [INFO] ===== Completeness check finished =====
[2023-03-19 05:20:58,578] [INFO] ===== Start GTDB Search =====
[2023-03-19 05:20:58,578] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10728/markers.fasta)
[2023-03-19 05:20:58,579] [INFO] Task started: Blastn
[2023-03-19 05:20:58,580] [INFO] Running command: blastn -query OceanDNA-b10728/markers.fasta -db /var/lib/cwl/stg72945ca1-c942-4d43-bf99-df7b78eded26/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10728/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:20:59,404] [INFO] Task succeeded: Blastn
[2023-03-19 05:20:59,405] [INFO] Selected 14 target genomes.
[2023-03-19 05:20:59,405] [INFO] Target genome list was writen to OceanDNA-b10728/target_genomes_gtdb.txt
[2023-03-19 05:20:59,447] [INFO] Task started: fastANI
[2023-03-19 05:20:59,447] [INFO] Running command: fastANI --query /var/lib/cwl/stg574ee88f-095f-4187-987a-23e9dc0f0837/OceanDNA-b10728.fa --refList OceanDNA-b10728/target_genomes_gtdb.txt --output OceanDNA-b10728/fastani_result_gtdb.tsv --threads 1
[2023-03-19 05:21:07,532] [INFO] Task succeeded: fastANI
[2023-03-19 05:21:07,540] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 05:21:07,540] [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_002707745.1	s__Marinirhabdus sp002707745	99.9912	750	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	99.79	99.79	0.83	0.83	2	conclusive
GCA_002337605.1	s__Marinirhabdus sp002337605	80.6174	609	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	98.69	98.69	0.95	0.95	2	-
GCF_003353425.1	s__Marinirhabdus gelatinilytica	78.9006	356	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002375495.1	s__Marinirhabdus sp002375495	78.4911	326	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	98.31	97.88	0.90	0.71	8	-
GCA_011044175.1	s__Marinirhabdus sp011044175	78.152	304	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002360635.1	s__Marixanthomonas sp002360635	77.2497	159	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	98.57	97.61	0.95	0.92	4	-
GCF_013394655.1	s__Winogradskyella schleiferi	77.058	71	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002966125.1	s__Pukyongia salina	77.0143	85	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pukyongia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003413745.1	s__Marixanthomonas ophiurae	76.9828	161	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813135.1	s__Altibacter sp002813135	76.9308	162	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310335.1	s__Jejuia pacifica	76.699	61	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002715485.1	s__Aequorivita sp002715485	76.5451	102	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.49	99.49	0.87	0.87	2	-
GCF_007997385.1	s__Seonamhaeicola algicola	76.0775	67	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002379985.1	s__Marixanthomonas sp002379985	76.0474	77	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	99.95	99.94	0.93	0.86	4	-
--------------------------------------------------------------------------------
[2023-03-19 05:21:07,541] [INFO] GTDB search result was written to OceanDNA-b10728/result_gtdb.tsv
[2023-03-19 05:21:07,541] [INFO] ===== GTDB Search completed =====
[2023-03-19 05:21:07,543] [INFO] DFAST_QC result json was written to OceanDNA-b10728/dqc_result.json
[2023-03-19 05:21:07,543] [INFO] DFAST_QC completed!
[2023-03-19 05:21:07,543] [INFO] Total running time: 0h1m34s