[2023-03-18 09:23:52,124] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:23:52,131] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:23:52,131] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a5b1023-4e53-4512-94f9-534b311f4ea3/dqc_reference
[2023-03-18 09:23:53,299] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:23:53,300] [INFO] Task started: Prodigal
[2023-03-18 09:23:53,300] [INFO] Running command: cat /var/lib/cwl/stgded82115-c502-4007-b98d-9db3a4f412d6/OceanDNA-b20911.fa | prodigal -d OceanDNA-b20911/cds.fna -a OceanDNA-b20911/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:24:18,463] [INFO] Task succeeded: Prodigal
[2023-03-18 09:24:18,464] [INFO] Task started: HMMsearch
[2023-03-18 09:24:18,464] [INFO] Running command: hmmsearch --tblout OceanDNA-b20911/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a5b1023-4e53-4512-94f9-534b311f4ea3/dqc_reference/reference_markers.hmm OceanDNA-b20911/protein.faa > /dev/null
[2023-03-18 09:24:18,728] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:24:18,728] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgded82115-c502-4007-b98d-9db3a4f412d6/OceanDNA-b20911.fa]
[2023-03-18 09:24:18,795] [INFO] Query marker FASTA was written to OceanDNA-b20911/markers.fasta
[2023-03-18 09:24:18,796] [INFO] Task started: Blastn
[2023-03-18 09:24:18,796] [INFO] Running command: blastn -query OceanDNA-b20911/markers.fasta -db /var/lib/cwl/stg8a5b1023-4e53-4512-94f9-534b311f4ea3/dqc_reference/reference_markers.fasta -out OceanDNA-b20911/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:24:19,521] [INFO] Task succeeded: Blastn
[2023-03-18 09:24:19,527] [INFO] Selected 18 target genomes.
[2023-03-18 09:24:19,528] [INFO] Target genome list was writen to OceanDNA-b20911/target_genomes.txt
[2023-03-18 09:24:19,541] [INFO] Task started: fastANI
[2023-03-18 09:24:19,541] [INFO] Running command: fastANI --query /var/lib/cwl/stgded82115-c502-4007-b98d-9db3a4f412d6/OceanDNA-b20911.fa --refList OceanDNA-b20911/target_genomes.txt --output OceanDNA-b20911/fastani_result.tsv --threads 1
[2023-03-18 09:24:38,302] [INFO] Task succeeded: fastANI
[2023-03-18 09:24:38,303] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a5b1023-4e53-4512-94f9-534b311f4ea3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:24:38,303] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a5b1023-4e53-4512-94f9-534b311f4ea3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:24:38,363] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:24:38,363] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 09:24:38,363] [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
Plesiocystis pacifica	strain=SIR-1	GCA_000170895.1	191768	191768	type	True	75.9713	170	1036	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	75.8141	198	1036	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	75.7688	202	1036	95	below_threshold
Jiangella mangrovi	strain=DSM 102122	GCA_014204975.1	1524084	1524084	type	True	74.8848	76	1036	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	74.7959	57	1036	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	74.7597	74	1036	95	below_threshold
Jiangella muralis	strain=DSM 45357	GCA_001270745.1	702383	702383	type	True	74.7036	80	1036	95	below_threshold
Micromonospora pallida	strain=DSM 43817	GCA_900090325.1	145854	145854	type	True	74.5542	59	1036	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 09:24:38,368] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20911/tc_result.tsv
[2023-03-18 09:24:38,372] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:24:38,372] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:24:38,372] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a5b1023-4e53-4512-94f9-534b311f4ea3/dqc_reference/checkm_data
[2023-03-18 09:24:38,373] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:24:38,383] [INFO] Task started: CheckM
[2023-03-18 09:24:38,383] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20911/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20911/checkm_input OceanDNA-b20911/checkm_result
[2023-03-18 09:25:42,908] [INFO] Task succeeded: CheckM
[2023-03-18 09:25:42,909] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.63%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 09:25:42,913] [INFO] ===== Completeness check finished =====
[2023-03-18 09:25:42,913] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:25:42,913] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20911/markers.fasta)
[2023-03-18 09:25:42,914] [INFO] Task started: Blastn
[2023-03-18 09:25:42,914] [INFO] Running command: blastn -query OceanDNA-b20911/markers.fasta -db /var/lib/cwl/stg8a5b1023-4e53-4512-94f9-534b311f4ea3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20911/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:25:43,923] [INFO] Task succeeded: Blastn
[2023-03-18 09:25:43,924] [INFO] Selected 15 target genomes.
[2023-03-18 09:25:43,924] [INFO] Target genome list was writen to OceanDNA-b20911/target_genomes_gtdb.txt
[2023-03-18 09:25:43,939] [INFO] Task started: fastANI
[2023-03-18 09:25:43,939] [INFO] Running command: fastANI --query /var/lib/cwl/stgded82115-c502-4007-b98d-9db3a4f412d6/OceanDNA-b20911.fa --refList OceanDNA-b20911/target_genomes_gtdb.txt --output OceanDNA-b20911/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:26:00,787] [INFO] Task succeeded: fastANI
[2023-03-18 09:26:00,794] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:26:00,794] [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_001464385.1	s__Ga0077550 sp001464385	76.5543	249	1036	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709225.1	s__Ga0077550 sp016709225	76.3638	252	1036	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	99.66	99.17	0.98	0.94	4	-
GCF_000170895.1	s__Plesiocystis pacifica	76.0073	166	1036	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Plesiocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013812955.1	s__Nannocystis sp013812955	75.9794	128	1036	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002994615.1	s__Enhygromyxa salina_A	75.8806	159	1036	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Enhygromyxa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714285.1	s__Nannocystis sp016714285	75.8324	154	1036	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	99.25	99.25	0.96	0.96	2	-
GCF_002343915.1	s__Nannocystis exedens	75.7834	198	1036	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	99.98	99.98	1.00	1.00	2	-
GCA_902826865.1	s__Ga0077550 sp902826865	75.7571	113	1036	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002994635.1	s__Enhygromyxa salina_B	75.6808	152	1036	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Enhygromyxa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737335.2	s__Enhygromyxa salina_C	75.4952	147	1036	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Enhygromyxa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712315.1	s__JADJRG01 sp016712315	75.4882	119	1036	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__JADJRG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:26:00,794] [INFO] GTDB search result was written to OceanDNA-b20911/result_gtdb.tsv
[2023-03-18 09:26:00,794] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:26:00,796] [INFO] DFAST_QC result json was written to OceanDNA-b20911/dqc_result.json
[2023-03-18 09:26:00,796] [INFO] DFAST_QC completed!
[2023-03-18 09:26:00,796] [INFO] Total running time: 0h2m9s