[2023-06-07 21:53:41,307] [INFO] DFAST_QC pipeline started.
[2023-06-07 21:53:41,309] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 21:53:41,309] [INFO] DQC Reference Directory: /var/lib/cwl/stg50d18384-e3d2-439b-a422-d14a953dc795/dqc_reference
[2023-06-07 21:53:42,760] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 21:53:42,761] [INFO] Task started: Prodigal
[2023-06-07 21:53:42,761] [INFO] Running command: gunzip -c /var/lib/cwl/stg3119db70-46d3-4a28-b0eb-ea05f9035cde/GCA_902752485.1_P1994_127_bin6_mag_fasta_genomic.fna.gz | prodigal -d GCA_902752485.1_P1994_127_bin6_mag_fasta_genomic.fna/cds.fna -a GCA_902752485.1_P1994_127_bin6_mag_fasta_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 21:53:49,051] [INFO] Task succeeded: Prodigal
[2023-06-07 21:53:49,052] [INFO] Task started: HMMsearch
[2023-06-07 21:53:49,052] [INFO] Running command: hmmsearch --tblout GCA_902752485.1_P1994_127_bin6_mag_fasta_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50d18384-e3d2-439b-a422-d14a953dc795/dqc_reference/reference_markers.hmm GCA_902752485.1_P1994_127_bin6_mag_fasta_genomic.fna/protein.faa > /dev/null
[2023-06-07 21:53:49,290] [INFO] Task succeeded: HMMsearch
[2023-06-07 21:53:49,291] [INFO] Found 6/6 markers.
[2023-06-07 21:53:49,314] [INFO] Query marker FASTA was written to GCA_902752485.1_P1994_127_bin6_mag_fasta_genomic.fna/markers.fasta
[2023-06-07 21:53:49,314] [INFO] Task started: Blastn
[2023-06-07 21:53:49,314] [INFO] Running command: blastn -query GCA_902752485.1_P1994_127_bin6_mag_fasta_genomic.fna/markers.fasta -db /var/lib/cwl/stg50d18384-e3d2-439b-a422-d14a953dc795/dqc_reference/reference_markers.fasta -out GCA_902752485.1_P1994_127_bin6_mag_fasta_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 21:53:49,974] [INFO] Task succeeded: Blastn
[2023-06-07 21:53:49,978] [INFO] Selected 13 target genomes.
[2023-06-07 21:53:49,978] [INFO] Target genome list was writen to GCA_902752485.1_P1994_127_bin6_mag_fasta_genomic.fna/target_genomes.txt
[2023-06-07 21:53:49,980] [INFO] Task started: fastANI
[2023-06-07 21:53:49,980] [INFO] Running command: fastANI --query /var/lib/cwl/stg3119db70-46d3-4a28-b0eb-ea05f9035cde/GCA_902752485.1_P1994_127_bin6_mag_fasta_genomic.fna.gz --refList GCA_902752485.1_P1994_127_bin6_mag_fasta_genomic.fna/target_genomes.txt --output GCA_902752485.1_P1994_127_bin6_mag_fasta_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 21:53:59,095] [INFO] Task succeeded: fastANI
[2023-06-07 21:53:59,095] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50d18384-e3d2-439b-a422-d14a953dc795/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 21:53:59,096] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50d18384-e3d2-439b-a422-d14a953dc795/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 21:53:59,113] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 21:53:59,114] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 21:53:59,114] [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
Lutibacter profundi	strain=LP1	GCA_001543325.1	1622118	1622118	type	True	80.4604	427	593	95	below_threshold
Lutibacter oceani	strain=JCM30924	GCA_003426875.1	1853311	1853311	type	True	79.9415	398	593	95	below_threshold
Lutibacter flavus	strain=DSM 27993	GCA_900188355.1	691689	691689	type	True	79.9121	414	593	95	below_threshold
Lutibacter oceani	strain=325-5	GCA_003384935.1	1853311	1853311	type	True	79.8982	409	593	95	below_threshold
Lutibacter maritimus	strain=DSM 24450	GCA_900116115.1	593133	593133	type	True	79.6579	379	593	95	below_threshold
Lutibacter agarilyticus	strain=DSM 29150	GCA_900188235.1	1109740	1109740	type	True	79.5385	357	593	95	below_threshold
Lutibacter citreus	strain=1KV19	GCA_003260195.1	2138210	2138210	type	True	79.4757	345	593	95	below_threshold
Lutibacter oricola	strain=DSM 24956	GCA_900106565.1	762486	762486	type	True	78.8873	321	593	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	77.3738	189	593	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	77.2874	166	593	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	77.1324	185	593	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	77.0635	163	593	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	77.0384	170	593	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 21:53:59,116] [INFO] DFAST Taxonomy check result was written to GCA_902752485.1_P1994_127_bin6_mag_fasta_genomic.fna/tc_result.tsv
[2023-06-07 21:53:59,117] [INFO] ===== Taxonomy check completed =====
[2023-06-07 21:53:59,117] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 21:53:59,118] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50d18384-e3d2-439b-a422-d14a953dc795/dqc_reference/checkm_data
[2023-06-07 21:53:59,120] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 21:53:59,148] [INFO] Task started: CheckM
[2023-06-07 21:53:59,148] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902752485.1_P1994_127_bin6_mag_fasta_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902752485.1_P1994_127_bin6_mag_fasta_genomic.fna/checkm_input GCA_902752485.1_P1994_127_bin6_mag_fasta_genomic.fna/checkm_result
[2023-06-07 21:54:24,393] [INFO] Task succeeded: CheckM
[2023-06-07 21:54:24,394] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-07 21:54:24,416] [INFO] ===== Completeness check finished =====
[2023-06-07 21:54:24,417] [INFO] ===== Start GTDB Search =====
[2023-06-07 21:54:24,417] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902752485.1_P1994_127_bin6_mag_fasta_genomic.fna/markers.fasta)
[2023-06-07 21:54:24,417] [INFO] Task started: Blastn
[2023-06-07 21:54:24,417] [INFO] Running command: blastn -query GCA_902752485.1_P1994_127_bin6_mag_fasta_genomic.fna/markers.fasta -db /var/lib/cwl/stg50d18384-e3d2-439b-a422-d14a953dc795/dqc_reference/reference_markers_gtdb.fasta -out GCA_902752485.1_P1994_127_bin6_mag_fasta_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 21:54:25,298] [INFO] Task succeeded: Blastn
[2023-06-07 21:54:25,303] [INFO] Selected 12 target genomes.
[2023-06-07 21:54:25,303] [INFO] Target genome list was writen to GCA_902752485.1_P1994_127_bin6_mag_fasta_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 21:54:25,310] [INFO] Task started: fastANI
[2023-06-07 21:54:25,310] [INFO] Running command: fastANI --query /var/lib/cwl/stg3119db70-46d3-4a28-b0eb-ea05f9035cde/GCA_902752485.1_P1994_127_bin6_mag_fasta_genomic.fna.gz --refList GCA_902752485.1_P1994_127_bin6_mag_fasta_genomic.fna/target_genomes_gtdb.txt --output GCA_902752485.1_P1994_127_bin6_mag_fasta_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 21:54:33,121] [INFO] Task succeeded: fastANI
[2023-06-07 21:54:33,132] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-07 21:54:33,133] [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_004195315.1	s__Lutibacter sp004195315	84.836	348	593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139515.1	s__Lutibacter sp013139515	82.3585	420	593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013041805.1	s__Lutibacter sp013041805	80.5699	418	593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001543325.1	s__Lutibacter profundi	80.4879	425	593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733285.1	s__Lutibacter sp002733285	80.4867	377	593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	97.79	97.79	0.89	0.89	2	-
GCF_900188355.1	s__Lutibacter flavus	79.9338	412	593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003384935.1	s__Lutibacter oceani	79.8982	409	593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016342705.1	s__Lutibacter sp016342705	79.8759	395	593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116115.1	s__Lutibacter maritimus	79.6513	380	593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646675.1	s__Lutibacter litoralis	79.5915	357	593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003260195.1	s__Lutibacter citreus	79.4465	347	593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012524075.1	s__Lutibacter sp012524075	79.1129	366	593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 21:54:33,135] [INFO] GTDB search result was written to GCA_902752485.1_P1994_127_bin6_mag_fasta_genomic.fna/result_gtdb.tsv
[2023-06-07 21:54:33,136] [INFO] ===== GTDB Search completed =====
[2023-06-07 21:54:33,141] [INFO] DFAST_QC result json was written to GCA_902752485.1_P1994_127_bin6_mag_fasta_genomic.fna/dqc_result.json
[2023-06-07 21:54:33,142] [INFO] DFAST_QC completed!
[2023-06-07 21:54:33,142] [INFO] Total running time: 0h0m52s