[2023-03-18 03:27:00,921] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:27:00,922] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:27:00,922] [INFO] DQC Reference Directory: /var/lib/cwl/stg99af98fe-8518-4a92-b3cd-6d2c60c40e07/dqc_reference
[2023-03-18 03:27:02,637] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:27:02,637] [INFO] Task started: Prodigal
[2023-03-18 03:27:02,637] [INFO] Running command: cat /var/lib/cwl/stg7671e18a-5b58-4e9c-806b-8c79ec0254af/OceanDNA-b17212.fa | prodigal -d OceanDNA-b17212/cds.fna -a OceanDNA-b17212/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:27:21,317] [INFO] Task succeeded: Prodigal
[2023-03-18 03:27:21,317] [INFO] Task started: HMMsearch
[2023-03-18 03:27:21,318] [INFO] Running command: hmmsearch --tblout OceanDNA-b17212/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99af98fe-8518-4a92-b3cd-6d2c60c40e07/dqc_reference/reference_markers.hmm OceanDNA-b17212/protein.faa > /dev/null
[2023-03-18 03:27:21,535] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:27:21,536] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7671e18a-5b58-4e9c-806b-8c79ec0254af/OceanDNA-b17212.fa]
[2023-03-18 03:27:21,566] [INFO] Query marker FASTA was written to OceanDNA-b17212/markers.fasta
[2023-03-18 03:27:21,566] [INFO] Task started: Blastn
[2023-03-18 03:27:21,566] [INFO] Running command: blastn -query OceanDNA-b17212/markers.fasta -db /var/lib/cwl/stg99af98fe-8518-4a92-b3cd-6d2c60c40e07/dqc_reference/reference_markers.fasta -out OceanDNA-b17212/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:27:22,186] [INFO] Task succeeded: Blastn
[2023-03-18 03:27:22,187] [INFO] Selected 21 target genomes.
[2023-03-18 03:27:22,187] [INFO] Target genome list was writen to OceanDNA-b17212/target_genomes.txt
[2023-03-18 03:27:22,200] [INFO] Task started: fastANI
[2023-03-18 03:27:22,200] [INFO] Running command: fastANI --query /var/lib/cwl/stg7671e18a-5b58-4e9c-806b-8c79ec0254af/OceanDNA-b17212.fa --refList OceanDNA-b17212/target_genomes.txt --output OceanDNA-b17212/fastani_result.tsv --threads 1
[2023-03-18 03:27:41,117] [INFO] Task succeeded: fastANI
[2023-03-18 03:27:41,117] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99af98fe-8518-4a92-b3cd-6d2c60c40e07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:27:41,117] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99af98fe-8518-4a92-b3cd-6d2c60c40e07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:27:41,126] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:27:41,126] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 03:27:41,127] [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
Longimicrobium terrae	strain=CECT 8660	GCA_014198875.1	1639882	1639882	type	True	75.6112	98	924	95	below_threshold
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	75.6096	98	924	95	below_threshold
Longimicrobium terrae	strain=DSM 29007	GCA_014202995.1	1639882	1639882	type	True	75.6004	99	924	95	below_threshold
Streptoalloteichus hindustanus	strain=DSM 44523	GCA_900129375.1	2017	2017	type	True	74.7754	79	924	95	below_threshold
Streptomyces megasporus	strain=NRRL B-16372	GCA_000718985.1	44060	44060	type	True	74.7752	77	924	95	below_threshold
Wenjunlia vitaminophila	strain=DSM 41686	GCA_000380165.1	76728	76728	type	True	74.7302	85	924	95	below_threshold
Wenjunlia vitaminophila	strain=ATCC 31673	GCA_001445835.1	76728	76728	type	True	74.7299	85	924	95	below_threshold
Streptomyces albidochromogenes	strain=DSM 41800	GCA_005981925.1	329524	329524	type	True	74.6575	68	924	95	below_threshold
Streptomyces resistomycificus	strain=NRRL ISP-5133	GCA_000716215.1	67356	67356	type	True	74.6456	73	924	95	below_threshold
Actinomadura barringtoniae	strain=GKU 128	GCA_017573505.1	1427535	1427535	type	True	74.6422	95	924	95	below_threshold
Saccharothrix tamanrassetensis	strain=CECT 8640	GCA_014203665.1	1051531	1051531	type	True	74.6385	92	924	95	below_threshold
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	74.6357	85	924	95	below_threshold
Nonomuraea solani	strain=CGMCC 4.7037	GCA_900108335.1	1144553	1144553	type	True	74.6349	127	924	95	below_threshold
Streptomyces chryseus	strain=JCM 4737	GCA_014650755.1	68186	68186	type	True	74.6318	78	924	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:27:41,127] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17212/tc_result.tsv
[2023-03-18 03:27:41,127] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:27:41,127] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:27:41,127] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99af98fe-8518-4a92-b3cd-6d2c60c40e07/dqc_reference/checkm_data
[2023-03-18 03:27:41,128] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:27:41,134] [INFO] Task started: CheckM
[2023-03-18 03:27:41,134] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17212/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17212/checkm_input OceanDNA-b17212/checkm_result
[2023-03-18 03:28:28,501] [INFO] Task succeeded: CheckM
[2023-03-18 03:28:28,501] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.81%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:28:28,505] [INFO] ===== Completeness check finished =====
[2023-03-18 03:28:28,505] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:28:28,505] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17212/markers.fasta)
[2023-03-18 03:28:28,505] [INFO] Task started: Blastn
[2023-03-18 03:28:28,505] [INFO] Running command: blastn -query OceanDNA-b17212/markers.fasta -db /var/lib/cwl/stg99af98fe-8518-4a92-b3cd-6d2c60c40e07/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17212/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:28:29,547] [INFO] Task succeeded: Blastn
[2023-03-18 03:28:29,548] [INFO] Selected 19 target genomes.
[2023-03-18 03:28:29,548] [INFO] Target genome list was writen to OceanDNA-b17212/target_genomes_gtdb.txt
[2023-03-18 03:28:29,565] [INFO] Task started: fastANI
[2023-03-18 03:28:29,566] [INFO] Running command: fastANI --query /var/lib/cwl/stg7671e18a-5b58-4e9c-806b-8c79ec0254af/OceanDNA-b17212.fa --refList OceanDNA-b17212/target_genomes_gtdb.txt --output OceanDNA-b17212/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:28:40,812] [INFO] Task succeeded: fastANI
[2023-03-18 03:28:40,822] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 03:28:40,823] [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_015492755.1	s__S146-37 sp015492755	77.0958	146	924	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__S146-37	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248075.1	s__SZUA-318 sp003248075	77.0539	200	924	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__SZUA-318	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873995.1	s__UBA2982 sp016873995	76.9869	103	924	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2982	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002885.1	s__UBA2589 sp013002885	76.7319	133	924	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2589	95.0	99.00	99.00	0.85	0.85	2	-
GCA_009692205.1	s__UBA2982 sp009692205	76.6265	100	924	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2982	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692665.1	s__SKNW01 sp007692665	76.4586	104	924	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__SKNW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692505.1	s__REBX01 sp007692505	76.2893	106	924	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__REBX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007126575.1	s__SLBA01 sp007126575	76.1906	84	924	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__SLBA01	95.0	99.74	99.74	0.94	0.94	2	-
GCA_007130605.1	s__SLBA01 sp007130605	76.1232	77	924	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__SLBA01	95.0	99.40	99.31	0.83	0.83	4	-
GCA_015664885.1	s__UBA1138 sp003447875	76.1007	93	924	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA1138	95.0	99.72	99.64	0.94	0.92	3	-
GCA_009843625.1	s__BD2-11 sp009843625	76.073	93	924	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__BD2-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007695195.1	s__PWLA01 sp007695195	75.9959	80	924	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__PWLA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003564295.1	s__PXFI01 sp003564295	75.8721	52	924	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__PXFI01	95.0	95.78	95.56	0.60	0.59	3	-
GCA_009840215.1	s__Bin94 sp009840215	75.8372	84	924	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__Bin94	95.0	99.38	99.00	0.93	0.91	6	-
GCA_007126035.1	s__SLCC01 sp007126035	75.7547	66	924	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__RSA9;g__SLCC01	95.0	99.93	99.93	0.94	0.94	2	-
GCA_007692605.1	s__SLBA01 sp007692605	75.6973	76	924	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__SLBA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242735.1	s__RSA9 sp003242735	75.4738	84	924	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__RSA9;g__RSA9	95.0	99.82	99.82	0.92	0.92	2	-
GCA_018316655.1	s__Nocardiopsis sp018316655	74.8437	89	924	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:28:40,823] [INFO] GTDB search result was written to OceanDNA-b17212/result_gtdb.tsv
[2023-03-18 03:28:40,823] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:28:40,825] [INFO] DFAST_QC result json was written to OceanDNA-b17212/dqc_result.json
[2023-03-18 03:28:40,825] [INFO] DFAST_QC completed!
[2023-03-18 03:28:40,825] [INFO] Total running time: 0h1m40s