[2023-03-19 00:29:45,955] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:29:45,955] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:29:45,955] [INFO] DQC Reference Directory: /var/lib/cwl/stga9665cfa-4117-497b-8941-6be278f2b760/dqc_reference
[2023-03-19 00:29:47,056] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:29:47,056] [INFO] Task started: Prodigal
[2023-03-19 00:29:47,056] [INFO] Running command: cat /var/lib/cwl/stge1eb7a44-e3f5-4b9e-8427-7c4c6dbd78e7/OceanDNA-b1137.fa | prodigal -d OceanDNA-b1137/cds.fna -a OceanDNA-b1137/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:29:59,872] [INFO] Task succeeded: Prodigal
[2023-03-19 00:29:59,873] [INFO] Task started: HMMsearch
[2023-03-19 00:29:59,873] [INFO] Running command: hmmsearch --tblout OceanDNA-b1137/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga9665cfa-4117-497b-8941-6be278f2b760/dqc_reference/reference_markers.hmm OceanDNA-b1137/protein.faa > /dev/null
[2023-03-19 00:30:00,028] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:30:00,029] [INFO] Found 6/6 markers.
[2023-03-19 00:30:00,044] [INFO] Query marker FASTA was written to OceanDNA-b1137/markers.fasta
[2023-03-19 00:30:00,045] [INFO] Task started: Blastn
[2023-03-19 00:30:00,045] [INFO] Running command: blastn -query OceanDNA-b1137/markers.fasta -db /var/lib/cwl/stga9665cfa-4117-497b-8941-6be278f2b760/dqc_reference/reference_markers.fasta -out OceanDNA-b1137/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:30:00,686] [INFO] Task succeeded: Blastn
[2023-03-19 00:30:00,687] [INFO] Selected 26 target genomes.
[2023-03-19 00:30:00,687] [INFO] Target genome list was writen to OceanDNA-b1137/target_genomes.txt
[2023-03-19 00:30:00,704] [INFO] Task started: fastANI
[2023-03-19 00:30:00,704] [INFO] Running command: fastANI --query /var/lib/cwl/stge1eb7a44-e3f5-4b9e-8427-7c4c6dbd78e7/OceanDNA-b1137.fa --refList OceanDNA-b1137/target_genomes.txt --output OceanDNA-b1137/fastani_result.tsv --threads 1
[2023-03-19 00:30:17,122] [INFO] Task succeeded: fastANI
[2023-03-19 00:30:17,122] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga9665cfa-4117-497b-8941-6be278f2b760/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:30:17,122] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga9665cfa-4117-497b-8941-6be278f2b760/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:30:17,130] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:30:17,130] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:30:17,130] [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
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.8397	134	673	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.7682	140	673	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.2354	100	673	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.8471	105	673	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	75.8156	64	673	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	75.7631	65	673	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	75.6439	88	673	95	below_threshold
Streptomyces palmae	strain=JCM 31289	GCA_004684805.1	1701085	1701085	type	True	75.3478	71	673	95	below_threshold
Modestobacter versicolor	strain=CP153-2	GCA_003226595.1	429133	429133	type	True	75.3334	67	673	95	below_threshold
Geodermatophilus nigrescens	strain=DSM 45408	GCA_900129495.1	1070870	1070870	type	True	75.2681	66	673	95	below_threshold
Modestobacter versicolor	strain=DSM 16678	GCA_014195485.1	429133	429133	type	True	75.254	74	673	95	below_threshold
Actinoplanes cyaneus	strain=NBRC 14990	GCA_016862095.1	52696	52696	type	True	75.149	90	673	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:30:17,131] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1137/tc_result.tsv
[2023-03-19 00:30:17,131] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:30:17,131] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:30:17,131] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga9665cfa-4117-497b-8941-6be278f2b760/dqc_reference/checkm_data
[2023-03-19 00:30:17,132] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:30:17,135] [INFO] Task started: CheckM
[2023-03-19 00:30:17,136] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1137/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1137/checkm_input OceanDNA-b1137/checkm_result
[2023-03-19 00:30:51,333] [INFO] Task succeeded: CheckM
[2023-03-19 00:30:51,333] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:30:51,335] [INFO] ===== Completeness check finished =====
[2023-03-19 00:30:51,335] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:30:51,336] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1137/markers.fasta)
[2023-03-19 00:30:51,336] [INFO] Task started: Blastn
[2023-03-19 00:30:51,336] [INFO] Running command: blastn -query OceanDNA-b1137/markers.fasta -db /var/lib/cwl/stga9665cfa-4117-497b-8941-6be278f2b760/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1137/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:30:52,349] [INFO] Task succeeded: Blastn
[2023-03-19 00:30:52,349] [INFO] Selected 9 target genomes.
[2023-03-19 00:30:52,350] [INFO] Target genome list was writen to OceanDNA-b1137/target_genomes_gtdb.txt
[2023-03-19 00:30:52,359] [INFO] Task started: fastANI
[2023-03-19 00:30:52,359] [INFO] Running command: fastANI --query /var/lib/cwl/stge1eb7a44-e3f5-4b9e-8427-7c4c6dbd78e7/OceanDNA-b1137.fa --refList OceanDNA-b1137/target_genomes_gtdb.txt --output OceanDNA-b1137/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:30:56,212] [INFO] Task succeeded: fastANI
[2023-03-19 00:30:56,218] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:30:56,218] [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_002727895.1	s__UBA9410 sp002727895	85.6113	433	673	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	97.12	97.12	0.93	0.93	2	-
GCA_016845305.1	s__UBA9410 sp016845305	84.9691	563	673	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239855.1	s__UBA9410 sp014239855	80.7689	437	673	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014237715.1	s__UBA9410 sp014237715	79.9434	399	673	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	98.52	98.52	0.97	0.97	2	-
GCA_003541675.1	s__UBA9410 sp003541675	79.0678	250	673	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002714485.1	s__UBA9410 sp002714485	79.0411	300	673	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012961035.1	s__UBA9410 sp012961035	78.9419	350	673	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	99.67	99.67	0.93	0.93	2	-
GCA_002329075.1	s__S20-B6 sp002329075	78.4302	264	673	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	98.53	97.43	0.90	0.85	7	-
--------------------------------------------------------------------------------
[2023-03-19 00:30:56,218] [INFO] GTDB search result was written to OceanDNA-b1137/result_gtdb.tsv
[2023-03-19 00:30:56,218] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:30:56,219] [INFO] DFAST_QC result json was written to OceanDNA-b1137/dqc_result.json
[2023-03-19 00:30:56,219] [INFO] DFAST_QC completed!
[2023-03-19 00:30:56,220] [INFO] Total running time: 0h1m10s