[2024-01-24 13:58:10,967] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:10,969] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:10,969] [INFO] DQC Reference Directory: /var/lib/cwl/stgad70b535-19be-4fdc-811f-cac1341bc36e/dqc_reference
[2024-01-24 13:58:12,374] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:12,375] [INFO] Task started: Prodigal
[2024-01-24 13:58:12,375] [INFO] Running command: gunzip -c /var/lib/cwl/stg88198b7f-226c-42ab-86c1-59294e1b6959/GCF_019375555.1_ASM1937555v1_genomic.fna.gz | prodigal -d GCF_019375555.1_ASM1937555v1_genomic.fna/cds.fna -a GCF_019375555.1_ASM1937555v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:29,012] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:29,013] [INFO] Task started: HMMsearch
[2024-01-24 13:58:29,013] [INFO] Running command: hmmsearch --tblout GCF_019375555.1_ASM1937555v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad70b535-19be-4fdc-811f-cac1341bc36e/dqc_reference/reference_markers.hmm GCF_019375555.1_ASM1937555v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:29,384] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:29,386] [INFO] Found 6/6 markers.
[2024-01-24 13:58:29,433] [INFO] Query marker FASTA was written to GCF_019375555.1_ASM1937555v1_genomic.fna/markers.fasta
[2024-01-24 13:58:29,434] [INFO] Task started: Blastn
[2024-01-24 13:58:29,434] [INFO] Running command: blastn -query GCF_019375555.1_ASM1937555v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad70b535-19be-4fdc-811f-cac1341bc36e/dqc_reference/reference_markers.fasta -out GCF_019375555.1_ASM1937555v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:30,311] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:30,315] [INFO] Selected 23 target genomes.
[2024-01-24 13:58:30,316] [INFO] Target genome list was writen to GCF_019375555.1_ASM1937555v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:30,326] [INFO] Task started: fastANI
[2024-01-24 13:58:30,326] [INFO] Running command: fastANI --query /var/lib/cwl/stg88198b7f-226c-42ab-86c1-59294e1b6959/GCF_019375555.1_ASM1937555v1_genomic.fna.gz --refList GCF_019375555.1_ASM1937555v1_genomic.fna/target_genomes.txt --output GCF_019375555.1_ASM1937555v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:47,944] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:47,945] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad70b535-19be-4fdc-811f-cac1341bc36e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:47,945] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad70b535-19be-4fdc-811f-cac1341bc36e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:47,966] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:58:47,966] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:58:47,967] [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
Roseobacter cerasinus	strain=AI77	GCA_009811755.1	2602289	2602289	type	True	78.9409	605	1621	95	below_threshold
Roseobacter denitrificans	strain=DSM 7001	GCA_900113215.1	2434	2434	type	True	78.2679	424	1621	95	below_threshold
Roseobacter ponti	strain=DSM 106830	GCA_012932215.1	1891787	1891787	type	True	78.2615	491	1621	95	below_threshold
Roseobacter denitrificans	strain=OCh 114	GCA_000014045.1	2434	2434	type	True	78.1943	442	1621	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	78.1022	504	1621	95	below_threshold
Roseobacter litoralis	strain=Och 149	GCA_000154785.2	42443	42443	type	True	78.0417	402	1621	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.6614	405	1621	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.659	413	1621	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	77.6372	358	1621	95	below_threshold
Sulfitobacter sediminilitoris	strain=JBTF-M27	GCA_010667575.1	2698830	2698830	type	True	77.6017	355	1621	95	below_threshold
Sulfitobacter aestuariivivens	strain=TSTF-M16	GCA_014763045.1	2766981	2766981	type	True	77.5452	319	1621	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	77.5018	279	1621	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	77.4844	325	1621	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	77.4175	329	1621	95	below_threshold
Marivita geojedonensis	strain=DPG-138	GCA_002115805.1	1123756	1123756	type	True	77.4142	272	1621	95	below_threshold
Marivita geojedonensis	strain=DSM 29432	GCA_003002975.1	1123756	1123756	type	True	77.3733	277	1621	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	77.2455	290	1621	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.2282	323	1621	95	below_threshold
Roseovarius gahaiensis	strain=GH877	GCA_011601345.1	2716691	2716691	type	True	77.0448	208	1621	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	76.5467	221	1621	95	below_threshold
Pseudogemmobacter bohemicus	strain=Cd-10	GCA_003290025.1	2250708	2250708	type	True	76.2893	156	1621	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:47,968] [INFO] DFAST Taxonomy check result was written to GCF_019375555.1_ASM1937555v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:47,969] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:47,969] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:47,969] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad70b535-19be-4fdc-811f-cac1341bc36e/dqc_reference/checkm_data
[2024-01-24 13:58:47,971] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:48,020] [INFO] Task started: CheckM
[2024-01-24 13:58:48,020] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019375555.1_ASM1937555v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019375555.1_ASM1937555v1_genomic.fna/checkm_input GCF_019375555.1_ASM1937555v1_genomic.fna/checkm_result
[2024-01-24 13:59:39,474] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:39,476] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:39,498] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:39,499] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:39,499] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019375555.1_ASM1937555v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:39,499] [INFO] Task started: Blastn
[2024-01-24 13:59:39,500] [INFO] Running command: blastn -query GCF_019375555.1_ASM1937555v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad70b535-19be-4fdc-811f-cac1341bc36e/dqc_reference/reference_markers_gtdb.fasta -out GCF_019375555.1_ASM1937555v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:40,964] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:40,969] [INFO] Selected 19 target genomes.
[2024-01-24 13:59:40,969] [INFO] Target genome list was writen to GCF_019375555.1_ASM1937555v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:41,001] [INFO] Task started: fastANI
[2024-01-24 13:59:41,001] [INFO] Running command: fastANI --query /var/lib/cwl/stg88198b7f-226c-42ab-86c1-59294e1b6959/GCF_019375555.1_ASM1937555v1_genomic.fna.gz --refList GCF_019375555.1_ASM1937555v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019375555.1_ASM1937555v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:56,143] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:56,166] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:59:56,167] [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
GCF_015644665.1	s__Roseobacter sp015644665	79.9499	735	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009811755.1	s__Roseobacter cerasinus	78.9409	605	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014337925.1	s__Roseobacter litoralis_A	78.4517	527	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932215.1	s__Roseobacter ponti	78.2615	491	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014045.1	s__Roseobacter denitrificans	78.2112	440	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_001650875.1	s__Sulfitobacter sp001650875	78.1116	424	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743885.1	s__Sulfitobacter sp001635605	78.0901	343	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	98.54	95.97	0.90	0.86	4	-
GCF_005887615.1	s__Sulfitobacter_E sabulilitoris	78.0884	506	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154785.2	s__Roseobacter litoralis	78.0406	401	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363555.1	s__Sulfitobacter sp009363555	77.9243	427	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886735.1	s__Sulfitobacter alexandrii	77.7888	397	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	77.6614	405	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_004358185.1	s__Antarcticimicrobium luteum	77.6289	359	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335545.1	s__Ascidiaceihabitans sp003335545	77.6184	383	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002115805.1	s__Marivita geojedonensis	77.4222	272	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003054325.1	s__Sulfitobacter mediterraneus	77.4175	329	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.52	96.39	0.88	0.86	71	-
GCF_007995245.1	s__Tateyamaria sp007995245	77.4084	368	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	77.3533	350	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_000622365.1	s__Sulfitobacter noctilucae	77.2455	290	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:56,168] [INFO] GTDB search result was written to GCF_019375555.1_ASM1937555v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:56,169] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:56,174] [INFO] DFAST_QC result json was written to GCF_019375555.1_ASM1937555v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:56,174] [INFO] DFAST_QC completed!
[2024-01-24 13:59:56,174] [INFO] Total running time: 0h1m45s