[2023-03-15 10:49:28,614] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:49:28,614] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:49:28,614] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf4dac6f-2ecb-471c-a992-047433e07a02/dqc_reference
[2023-03-15 10:49:29,799] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:49:29,800] [INFO] Task started: Prodigal
[2023-03-15 10:49:29,800] [INFO] Running command: cat /var/lib/cwl/stgfa33041a-16b0-4dea-aa36-c58720d7a656/OceanDNA-b10517.fa | prodigal -d OceanDNA-b10517/cds.fna -a OceanDNA-b10517/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:49:41,356] [INFO] Task succeeded: Prodigal
[2023-03-15 10:49:41,356] [INFO] Task started: HMMsearch
[2023-03-15 10:49:41,357] [INFO] Running command: hmmsearch --tblout OceanDNA-b10517/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf4dac6f-2ecb-471c-a992-047433e07a02/dqc_reference/reference_markers.hmm OceanDNA-b10517/protein.faa > /dev/null
[2023-03-15 10:49:41,592] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:49:41,593] [INFO] Found 6/6 markers.
[2023-03-15 10:49:41,605] [INFO] Query marker FASTA was written to OceanDNA-b10517/markers.fasta
[2023-03-15 10:49:41,605] [INFO] Task started: Blastn
[2023-03-15 10:49:41,605] [INFO] Running command: blastn -query OceanDNA-b10517/markers.fasta -db /var/lib/cwl/stgdf4dac6f-2ecb-471c-a992-047433e07a02/dqc_reference/reference_markers.fasta -out OceanDNA-b10517/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:49:42,186] [INFO] Task succeeded: Blastn
[2023-03-15 10:49:42,186] [INFO] Selected 34 target genomes.
[2023-03-15 10:49:42,187] [INFO] Target genome list was writen to OceanDNA-b10517/target_genomes.txt
[2023-03-15 10:49:42,205] [INFO] Task started: fastANI
[2023-03-15 10:49:42,205] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa33041a-16b0-4dea-aa36-c58720d7a656/OceanDNA-b10517.fa --refList OceanDNA-b10517/target_genomes.txt --output OceanDNA-b10517/fastani_result.tsv --threads 1
[2023-03-15 10:50:04,002] [INFO] Task succeeded: fastANI
[2023-03-15 10:50:04,002] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf4dac6f-2ecb-471c-a992-047433e07a02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:50:04,002] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf4dac6f-2ecb-471c-a992-047433e07a02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:50:04,012] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:50:04,012] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 10:50:04,012] [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
Yeosuana marina	strain=JLT21	GCA_011762485.1	1565536	1565536	type	True	76.648	66	547	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	76.5638	60	547	95	below_threshold
Mesoflavibacter profundi	strain=YC1039	GCA_014764305.1	2708110	2708110	type	True	76.4391	50	547	95	below_threshold
Hanstruepera ponticola	strain=MM-14	GCA_012931685.1	2042995	2042995	type	True	76.4073	65	547	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.3429	54	547	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.3227	57	547	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	76.125	63	547	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	76.1062	51	547	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	76.1062	51	547	95	below_threshold
Tamlana sedimentorum	strain=JCM 19808	GCA_000943565.1	1435349	1435349	type	True	76.057	57	547	95	below_threshold
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	76.0375	56	547	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	76.0258	61	547	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	75.9762	66	547	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	75.9613	55	547	95	below_threshold
Algibacter lectus	strain=DSM 15365	GCA_900112395.1	221126	221126	type	True	75.9131	50	547	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 10:50:04,012] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10517/tc_result.tsv
[2023-03-15 10:50:04,012] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:50:04,012] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:50:04,012] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf4dac6f-2ecb-471c-a992-047433e07a02/dqc_reference/checkm_data
[2023-03-15 10:50:04,013] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:50:04,021] [INFO] Task started: CheckM
[2023-03-15 10:50:04,021] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10517/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10517/checkm_input OceanDNA-b10517/checkm_result
[2023-03-15 10:50:37,321] [INFO] Task succeeded: CheckM
[2023-03-15 10:50:37,322] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 10:50:37,324] [INFO] ===== Completeness check finished =====
[2023-03-15 10:50:37,324] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:50:37,324] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10517/markers.fasta)
[2023-03-15 10:50:37,325] [INFO] Task started: Blastn
[2023-03-15 10:50:37,325] [INFO] Running command: blastn -query OceanDNA-b10517/markers.fasta -db /var/lib/cwl/stgdf4dac6f-2ecb-471c-a992-047433e07a02/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10517/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:50:38,092] [INFO] Task succeeded: Blastn
[2023-03-15 10:50:38,093] [INFO] Selected 33 target genomes.
[2023-03-15 10:50:38,093] [INFO] Target genome list was writen to OceanDNA-b10517/target_genomes_gtdb.txt
[2023-03-15 10:50:38,129] [INFO] Task started: fastANI
[2023-03-15 10:50:38,129] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa33041a-16b0-4dea-aa36-c58720d7a656/OceanDNA-b10517.fa --refList OceanDNA-b10517/target_genomes_gtdb.txt --output OceanDNA-b10517/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:50:52,506] [INFO] Task succeeded: fastANI
[2023-03-15 10:50:52,517] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:50:52,517] [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_001735715.1	s__GCA001735715 sp001735715	77.2012	148	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA001735715	95.0	98.19	98.19	0.84	0.84	2	-
GCA_002725015.1	s__UBA3537 sp002725015	77.0276	81	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	96.56	95.66	0.77	0.72	3	-
GCA_002709185.1	s__UBA3537 sp002709185	76.8433	85	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	98.67	98.67	0.76	0.76	2	-
GCA_002690085.1	s__UBA3537 sp002690085	76.7704	84	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997385.1	s__Seonamhaeicola algicola	76.5638	60	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151975.1	s__PRS1 sp013151975	76.5353	58	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__PRS1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181825.1	s__Hel1-33-131 sp905181825	76.4297	69	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	99.01	99.01	0.77	0.77	2	-
GCA_018608725.1	s__Hel1-33-131 sp018608725	76.3539	72	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001735745.1	s__Hel1-33-131 sp001735745	76.3339	84	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722255.1	s__Winogradskyella sp002722255	76.2932	52	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.90	99.90	0.80	0.80	2	-
GCF_014526325.1	s__Psychroserpens algicola	76.2823	50	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971785.1	s__Seonamhaeicola sp001971785	76.2205	67	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479095.1	s__Hel1-33-131 sp905479095	76.1674	78	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608705.1	s__Hel1-33-131 sp018608705	76.1414	60	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	99.44	99.44	0.94	0.94	2	-
GCA_003712105.1	s__Winogradskyella sp003712105	76.119	51	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014297365.1	s__Winogradskyella echinorum	76.1062	51	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018608625.1	s__Hel1-33-131 sp018608625	76.0786	61	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	98.93	97.98	0.88	0.82	3	-
GCF_008056315.1	s__Seonamhaeicola maritimus	75.9762	66	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741945.1	s__Wocania sp002741945	75.8336	60	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 10:50:52,517] [INFO] GTDB search result was written to OceanDNA-b10517/result_gtdb.tsv
[2023-03-15 10:50:52,517] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:50:52,519] [INFO] DFAST_QC result json was written to OceanDNA-b10517/dqc_result.json
[2023-03-15 10:50:52,519] [INFO] DFAST_QC completed!
[2023-03-15 10:50:52,519] [INFO] Total running time: 0h1m24s