[2023-03-18 08:44:04,391] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:44:04,391] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:44:04,391] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b1f5722-c154-42b8-bbe2-c421e1e2f1bd/dqc_reference
[2023-03-18 08:44:05,522] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:44:05,523] [INFO] Task started: Prodigal
[2023-03-18 08:44:05,523] [INFO] Running command: cat /var/lib/cwl/stg5eb32760-e601-4ff5-9b38-66c46f4ab7d6/OceanDNA-b23023.fa | prodigal -d OceanDNA-b23023/cds.fna -a OceanDNA-b23023/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:44:43,864] [INFO] Task succeeded: Prodigal
[2023-03-18 08:44:43,865] [INFO] Task started: HMMsearch
[2023-03-18 08:44:43,865] [INFO] Running command: hmmsearch --tblout OceanDNA-b23023/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b1f5722-c154-42b8-bbe2-c421e1e2f1bd/dqc_reference/reference_markers.hmm OceanDNA-b23023/protein.faa > /dev/null
[2023-03-18 08:44:44,082] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:44:44,083] [INFO] Found 6/6 markers.
[2023-03-18 08:44:44,110] [INFO] Query marker FASTA was written to OceanDNA-b23023/markers.fasta
[2023-03-18 08:44:44,111] [INFO] Task started: Blastn
[2023-03-18 08:44:44,111] [INFO] Running command: blastn -query OceanDNA-b23023/markers.fasta -db /var/lib/cwl/stg1b1f5722-c154-42b8-bbe2-c421e1e2f1bd/dqc_reference/reference_markers.fasta -out OceanDNA-b23023/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:44:44,669] [INFO] Task succeeded: Blastn
[2023-03-18 08:44:44,670] [INFO] Selected 24 target genomes.
[2023-03-18 08:44:44,670] [INFO] Target genome list was writen to OceanDNA-b23023/target_genomes.txt
[2023-03-18 08:44:44,684] [INFO] Task started: fastANI
[2023-03-18 08:44:44,684] [INFO] Running command: fastANI --query /var/lib/cwl/stg5eb32760-e601-4ff5-9b38-66c46f4ab7d6/OceanDNA-b23023.fa --refList OceanDNA-b23023/target_genomes.txt --output OceanDNA-b23023/fastani_result.tsv --threads 1
[2023-03-18 08:45:03,966] [INFO] Task succeeded: fastANI
[2023-03-18 08:45:03,966] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b1f5722-c154-42b8-bbe2-c421e1e2f1bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:45:03,967] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b1f5722-c154-42b8-bbe2-c421e1e2f1bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:45:03,975] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:45:03,975] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:45:03,976] [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
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	74.8388	98	1523	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	74.8334	112	1523	95	below_threshold
Paludisphaera borealis	strain=PX4	GCA_001956985.1	1387353	1387353	type	True	74.8284	82	1523	95	below_threshold
Phenylobacterium zucineum	strain=HLK1	GCA_000017265.1	284016	284016	type	True	74.8149	51	1523	95	below_threshold
Paludisphaera rhizosphaereae	strain=JC665	GCA_011065895.1	2711216	2711216	type	True	74.8102	71	1523	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	74.7514	90	1523	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	74.7236	59	1523	95	below_threshold
Lysobacter segetis	strain=17J68-2	GCA_004359965.1	2492394	2492394	type	True	74.7007	64	1523	95	below_threshold
Mycolicibacterium elephantis	strain=DSM 44368	GCA_004014805.1	81858	81858	type	True	74.677	50	1523	95	below_threshold
Halomarina salina	strain=ZS-57-S	GCA_023074835.1	1872699	1872699	type	True	74.6728	54	1523	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	74.6123	55	1523	95	below_threshold
Bradyrhizobium betae	strain=PL7HG1	GCA_008932115.1	244734	244734	type	True	74.6057	57	1523	95	below_threshold
Azospirillum doebereinerae	strain=GSF71	GCA_003989665.1	92933	92933	type	True	74.5754	63	1523	95	below_threshold
Bradyrhizobium yuanmingense	strain=CCBAU 10071	GCA_900094575.1	108015	108015	type	True	74.5586	82	1523	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:45:03,976] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23023/tc_result.tsv
[2023-03-18 08:45:03,976] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:45:03,976] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:45:03,976] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b1f5722-c154-42b8-bbe2-c421e1e2f1bd/dqc_reference/checkm_data
[2023-03-18 08:45:03,977] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:45:03,982] [INFO] Task started: CheckM
[2023-03-18 08:45:03,982] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23023/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23023/checkm_input OceanDNA-b23023/checkm_result
[2023-03-18 08:46:35,785] [INFO] Task succeeded: CheckM
[2023-03-18 08:46:35,786] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 08:46:35,840] [INFO] ===== Completeness check finished =====
[2023-03-18 08:46:35,840] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:46:35,840] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23023/markers.fasta)
[2023-03-18 08:46:35,841] [INFO] Task started: Blastn
[2023-03-18 08:46:35,842] [INFO] Running command: blastn -query OceanDNA-b23023/markers.fasta -db /var/lib/cwl/stg1b1f5722-c154-42b8-bbe2-c421e1e2f1bd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23023/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:46:36,867] [INFO] Task succeeded: Blastn
[2023-03-18 08:46:36,870] [INFO] Selected 20 target genomes.
[2023-03-18 08:46:36,870] [INFO] Target genome list was writen to OceanDNA-b23023/target_genomes_gtdb.txt
[2023-03-18 08:46:36,893] [INFO] Task started: fastANI
[2023-03-18 08:46:36,893] [INFO] Running command: fastANI --query /var/lib/cwl/stg5eb32760-e601-4ff5-9b38-66c46f4ab7d6/OceanDNA-b23023.fa --refList OceanDNA-b23023/target_genomes_gtdb.txt --output OceanDNA-b23023/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:46:52,312] [INFO] Task succeeded: fastANI
[2023-03-18 08:46:52,321] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:46:52,321] [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_013140785.1	s__JABFRZ01 sp013140785	76.7651	156	1523	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JABFRZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007750655.1	s__Pla163 sp007750655	76.7188	228	1523	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__Pla163	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826945.1	s__RBC036 sp902826945	76.6314	282	1523	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__RBC036	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011053145.1	s__DRLC01 sp011053145	76.607	175	1523	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__DRLC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903928115.1	s__F1-120-MAGs118 sp903928115	76.5246	209	1523	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__F1-120-MAGs118	95.0	99.83	99.80	0.95	0.95	3	-
GCA_009691855.1	s__JABFRZ01 sp009691855	76.4862	209	1523	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JABFRZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007751255.1	s__Pla86 sp007751255	76.4753	225	1523	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__Pla86	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016872755.1	s__GW928-bin9 sp016872755	76.3705	179	1523	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GW928-bin9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709875.1	s__JADJLZ01 sp016709875	76.2325	242	1523	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJLZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525785.1	s__WYBT01 sp011525785	76.1826	249	1523	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__WYBT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779205.1	s__GCA-2862085 sp016779205	76.171	139	1523	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795205.1	s__JAEUHZ01 sp016795205	75.9772	204	1523	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JAEUHZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004296785.1	s__GW928-bin9 sp004296785	75.9457	186	1523	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GW928-bin9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714045.1	s__JADJNY01 sp016714045	75.7993	283	1523	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJNY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480285.1	s__GCA-2862085 sp905480285	75.6188	133	1523	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001676615.1	s__Labrys sp001676615	74.6411	53	1523	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Labraceae;g__Labrys	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:46:52,322] [INFO] GTDB search result was written to OceanDNA-b23023/result_gtdb.tsv
[2023-03-18 08:46:52,323] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:46:52,325] [INFO] DFAST_QC result json was written to OceanDNA-b23023/dqc_result.json
[2023-03-18 08:46:52,325] [INFO] DFAST_QC completed!
[2023-03-18 08:46:52,325] [INFO] Total running time: 0h2m48s