[2023-03-19 03:50:07,839] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:50:07,839] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:50:07,839] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b89eea1-527e-45fb-93c6-f99bd8f79e0f/dqc_reference
[2023-03-19 03:50:09,606] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:50:09,607] [INFO] Task started: Prodigal
[2023-03-19 03:50:09,607] [INFO] Running command: cat /var/lib/cwl/stg902a1c69-355a-48b1-a354-ad686a4f2a28/OceanDNA-b1825.fa | prodigal -d OceanDNA-b1825/cds.fna -a OceanDNA-b1825/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:50:33,334] [INFO] Task succeeded: Prodigal
[2023-03-19 03:50:33,334] [INFO] Task started: HMMsearch
[2023-03-19 03:50:33,334] [INFO] Running command: hmmsearch --tblout OceanDNA-b1825/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b89eea1-527e-45fb-93c6-f99bd8f79e0f/dqc_reference/reference_markers.hmm OceanDNA-b1825/protein.faa > /dev/null
[2023-03-19 03:50:33,614] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:50:33,614] [INFO] Found 6/6 markers.
[2023-03-19 03:50:33,640] [INFO] Query marker FASTA was written to OceanDNA-b1825/markers.fasta
[2023-03-19 03:50:33,640] [INFO] Task started: Blastn
[2023-03-19 03:50:33,640] [INFO] Running command: blastn -query OceanDNA-b1825/markers.fasta -db /var/lib/cwl/stg1b89eea1-527e-45fb-93c6-f99bd8f79e0f/dqc_reference/reference_markers.fasta -out OceanDNA-b1825/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:50:34,472] [INFO] Task succeeded: Blastn
[2023-03-19 03:50:34,473] [INFO] Selected 15 target genomes.
[2023-03-19 03:50:34,473] [INFO] Target genome list was writen to OceanDNA-b1825/target_genomes.txt
[2023-03-19 03:50:34,481] [INFO] Task started: fastANI
[2023-03-19 03:50:34,481] [INFO] Running command: fastANI --query /var/lib/cwl/stg902a1c69-355a-48b1-a354-ad686a4f2a28/OceanDNA-b1825.fa --refList OceanDNA-b1825/target_genomes.txt --output OceanDNA-b1825/fastani_result.tsv --threads 1
[2023-03-19 03:50:46,238] [INFO] Task succeeded: fastANI
[2023-03-19 03:50:46,239] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b89eea1-527e-45fb-93c6-f99bd8f79e0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:50:46,239] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b89eea1-527e-45fb-93c6-f99bd8f79e0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:50:46,248] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:50:46,249] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 03:50:46,249] [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	78.4563	532	1287	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	77.8957	428	1287	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	77.4722	460	1287	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.1426	408	1287	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.1327	292	1287	95	below_threshold
Motilibacter peucedani	strain=RP-AC37	GCA_003634695.1	598650	598650	type	True	75.3749	328	1287	95	below_threshold
Demequina rhizosphaerae	strain=NBRC 109397	GCA_000971255.1	1638985	1638985	type	True	75.3368	175	1287	95	below_threshold
Demequina gelatinilytica	strain=NBRC 109390	GCA_000971115.1	1638980	1638980	type	True	75.2024	158	1287	95	below_threshold
Nocardiopsis chromatogenes	strain=YIM 90109	GCA_000341185.1	280239	280239	type	True	75.1903	372	1287	95	below_threshold
Jiangella anatolica	strain=GTF31	GCA_003236295.1	2670374	2670374	type	True	75.1035	419	1287	95	below_threshold
Georgenia thermotolerans	strain=NBRC 104148	GCA_009193185.1	527326	527326	type	True	75.046	362	1287	95	below_threshold
Georgenia thermotolerans	strain=DSM 21501	GCA_009299305.1	527326	527326	type	True	75.0413	332	1287	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	74.8938	174	1287	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	74.7041	82	1287	95	below_threshold
Halofilum ochraceum	strain=XJ16	GCA_001614315.2	1611323	1611323	type	True	74.595	60	1287	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 03:50:46,249] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1825/tc_result.tsv
[2023-03-19 03:50:46,249] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:50:46,249] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:50:46,249] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b89eea1-527e-45fb-93c6-f99bd8f79e0f/dqc_reference/checkm_data
[2023-03-19 03:50:46,250] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:50:46,255] [INFO] Task started: CheckM
[2023-03-19 03:50:46,255] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1825/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1825/checkm_input OceanDNA-b1825/checkm_result
[2023-03-19 03:52:11,805] [INFO] Task succeeded: CheckM
[2023-03-19 03:52:11,806] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:52:11,809] [INFO] ===== Completeness check finished =====
[2023-03-19 03:52:11,809] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:52:11,809] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1825/markers.fasta)
[2023-03-19 03:52:11,810] [INFO] Task started: Blastn
[2023-03-19 03:52:11,810] [INFO] Running command: blastn -query OceanDNA-b1825/markers.fasta -db /var/lib/cwl/stg1b89eea1-527e-45fb-93c6-f99bd8f79e0f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1825/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:52:13,154] [INFO] Task succeeded: Blastn
[2023-03-19 03:52:13,155] [INFO] Selected 18 target genomes.
[2023-03-19 03:52:13,155] [INFO] Target genome list was writen to OceanDNA-b1825/target_genomes_gtdb.txt
[2023-03-19 03:52:13,192] [INFO] Task started: fastANI
[2023-03-19 03:52:13,192] [INFO] Running command: fastANI --query /var/lib/cwl/stg902a1c69-355a-48b1-a354-ad686a4f2a28/OceanDNA-b1825.fa --refList OceanDNA-b1825/target_genomes_gtdb.txt --output OceanDNA-b1825/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:52:26,249] [INFO] Task succeeded: fastANI
[2023-03-19 03:52:26,260] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 03:52:26,261] [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_018969405.1	s__F1-20-MAGs160 sp018969405	78.0633	284	1287	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__F1-20-MAGs160	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014805525.1	s__Rhabdothermincola sediminis	77.9107	426	1287	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__Rhabdothermincola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882935.1	s__JADGOP01 sp017882935	77.8992	315	1287	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JADGOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401565.1	s__M30B73 sp018401565	77.7446	308	1287	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__M30B73	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794585.1	s__JAEUJM01 sp016794585	77.7394	571	1287	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAEUJM01;g__JAEUJM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002403895.1	s__UBA4742 sp002403895	77.7244	362	1287	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__UBA4742	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019048865.1	s__Aquihabitans sp019048865	77.5533	601	1287	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__Aquihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009650215.1	s__Actinomarinicola tropica	77.5035	453	1287	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017577565.1	s__ZC4RG19 sp017577565	77.4722	512	1287	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716005.1	s__JADJXE01 sp016716005	77.413	496	1287	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JADJXE01;g__JADJXE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012513855.1	s__JAAZBK01 sp012513855	77.3506	328	1287	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAAZBK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185275.1	s__JACPNX01 sp016185275	77.3186	383	1287	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JACPNX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004366205.1	s__SIRW01 sp004366205	77.301	483	1287	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SIRW01;g__SIRW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016781135.1	s__LC5-5 sp016781135	77.2622	290	1287	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CADCSY01;g__LC5-5	95.0	99.16	98.25	0.93	0.85	8	-
GCA_012730075.1	s__JAAYBP01 sp012730075	77.0988	385	1287	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAAYBP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805555.1	s__CADCSY01 sp902805555	76.9434	348	1287	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CADCSY01;g__CADCSY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903953195.1	s__SXMI01 sp903953195	76.9175	244	1287	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SXMI01	95.0	98.58	98.55	0.81	0.80	3	-
GCA_003697065.1	s__J010 sp003697065	76.8988	316	1287	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__J010	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 03:52:26,261] [INFO] GTDB search result was written to OceanDNA-b1825/result_gtdb.tsv
[2023-03-19 03:52:26,261] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:52:26,263] [INFO] DFAST_QC result json was written to OceanDNA-b1825/dqc_result.json
[2023-03-19 03:52:26,263] [INFO] DFAST_QC completed!
[2023-03-19 03:52:26,263] [INFO] Total running time: 0h2m18s