[2024-01-25 18:16:35,378] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:16:35,379] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:16:35,379] [INFO] DQC Reference Directory: /var/lib/cwl/stgcbee586a-d8ca-4e3e-af98-3b011e9559e8/dqc_reference
[2024-01-25 18:16:36,495] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:16:36,495] [INFO] Task started: Prodigal
[2024-01-25 18:16:36,496] [INFO] Running command: gunzip -c /var/lib/cwl/stgbc3c7605-4f00-4822-89d0-8c76539bcf85/GCF_021728415.1_ASM2172841v1_genomic.fna.gz | prodigal -d GCF_021728415.1_ASM2172841v1_genomic.fna/cds.fna -a GCF_021728415.1_ASM2172841v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:16:45,074] [INFO] Task succeeded: Prodigal
[2024-01-25 18:16:45,075] [INFO] Task started: HMMsearch
[2024-01-25 18:16:45,075] [INFO] Running command: hmmsearch --tblout GCF_021728415.1_ASM2172841v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcbee586a-d8ca-4e3e-af98-3b011e9559e8/dqc_reference/reference_markers.hmm GCF_021728415.1_ASM2172841v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:16:45,300] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:16:45,301] [INFO] Found 6/6 markers.
[2024-01-25 18:16:45,327] [INFO] Query marker FASTA was written to GCF_021728415.1_ASM2172841v1_genomic.fna/markers.fasta
[2024-01-25 18:16:45,327] [INFO] Task started: Blastn
[2024-01-25 18:16:45,327] [INFO] Running command: blastn -query GCF_021728415.1_ASM2172841v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcbee586a-d8ca-4e3e-af98-3b011e9559e8/dqc_reference/reference_markers.fasta -out GCF_021728415.1_ASM2172841v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:16:45,973] [INFO] Task succeeded: Blastn
[2024-01-25 18:16:45,976] [INFO] Selected 19 target genomes.
[2024-01-25 18:16:45,976] [INFO] Target genome list was writen to GCF_021728415.1_ASM2172841v1_genomic.fna/target_genomes.txt
[2024-01-25 18:16:45,986] [INFO] Task started: fastANI
[2024-01-25 18:16:45,986] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc3c7605-4f00-4822-89d0-8c76539bcf85/GCF_021728415.1_ASM2172841v1_genomic.fna.gz --refList GCF_021728415.1_ASM2172841v1_genomic.fna/target_genomes.txt --output GCF_021728415.1_ASM2172841v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:16:59,937] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:59,937] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcbee586a-d8ca-4e3e-af98-3b011e9559e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:16:59,938] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcbee586a-d8ca-4e3e-af98-3b011e9559e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:16:59,949] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:16:59,949] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:16:59,949] [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
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	80.509	586	1088	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	80.4655	595	1088	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	79.261	553	1088	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	78.8922	479	1088	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	78.8824	481	1088	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	78.8615	484	1088	95	below_threshold
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	78.8556	430	1088	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	78.69	467	1088	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	78.5567	480	1088	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	78.4748	428	1088	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	78.3584	375	1088	95	below_threshold
Tamlana haliotis	strain=B1N29	GCA_008806375.1	2614804	2614804	type	True	78.3471	323	1088	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	78.3398	431	1088	95	below_threshold
Flavivirga eckloniae	strain=ECD14	GCA_002886045.1	1803846	1803846	type	True	78.2393	431	1088	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	78.1894	406	1088	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	78.0787	339	1088	95	below_threshold
Yeosuana marina	strain=JLT21	GCA_011762485.1	1565536	1565536	type	True	78.0581	394	1088	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	77.9858	279	1088	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.8943	332	1088	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:16:59,950] [INFO] DFAST Taxonomy check result was written to GCF_021728415.1_ASM2172841v1_genomic.fna/tc_result.tsv
[2024-01-25 18:16:59,951] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:16:59,951] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:16:59,951] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcbee586a-d8ca-4e3e-af98-3b011e9559e8/dqc_reference/checkm_data
[2024-01-25 18:16:59,952] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:16:59,987] [INFO] Task started: CheckM
[2024-01-25 18:16:59,987] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021728415.1_ASM2172841v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021728415.1_ASM2172841v1_genomic.fna/checkm_input GCF_021728415.1_ASM2172841v1_genomic.fna/checkm_result
[2024-01-25 18:17:28,903] [INFO] Task succeeded: CheckM
[2024-01-25 18:17:28,905] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:17:28,923] [INFO] ===== Completeness check finished =====
[2024-01-25 18:17:28,923] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:17:28,923] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021728415.1_ASM2172841v1_genomic.fna/markers.fasta)
[2024-01-25 18:17:28,924] [INFO] Task started: Blastn
[2024-01-25 18:17:28,924] [INFO] Running command: blastn -query GCF_021728415.1_ASM2172841v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcbee586a-d8ca-4e3e-af98-3b011e9559e8/dqc_reference/reference_markers_gtdb.fasta -out GCF_021728415.1_ASM2172841v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:17:29,882] [INFO] Task succeeded: Blastn
[2024-01-25 18:17:29,885] [INFO] Selected 16 target genomes.
[2024-01-25 18:17:29,886] [INFO] Target genome list was writen to GCF_021728415.1_ASM2172841v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:17:29,897] [INFO] Task started: fastANI
[2024-01-25 18:17:29,898] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc3c7605-4f00-4822-89d0-8c76539bcf85/GCF_021728415.1_ASM2172841v1_genomic.fna.gz --refList GCF_021728415.1_ASM2172841v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021728415.1_ASM2172841v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:17:42,533] [INFO] Task succeeded: fastANI
[2024-01-25 18:17:42,544] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:17:42,544] [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_900114265.1	s__Flaviramulus basaltis	80.5534	634	1088	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141715.1	s__Arenitalea lutea	80.5098	587	1088	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013001275.1	s__Flaviramulus sp013001275	79.645	473	1088	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	79.2705	551	1088	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789235.1	s__Wocania ichthyoenteri	79.1918	515	1088	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741945.1	s__Wocania sp002741945	78.9936	475	1088	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015355625.1	s__Tamlana_A sp015355625	78.8392	404	1088	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480415.1	s__Algibacter_B sp905480415	78.7853	434	1088	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747085.1	s__Algibacter_C aquaticus	78.7651	451	1088	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971785.1	s__Seonamhaeicola sp001971785	78.5892	433	1088	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791695.1	s__Flavivirga rizhaonensis	78.548	481	1088	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860245.1	s__Tamlana_A agarivorans_A	78.488	367	1088	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008056315.1	s__Seonamhaeicola maritimus	78.3487	430	1088	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002886045.1	s__Flavivirga eckloniae	78.2495	428	1088	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997385.1	s__Seonamhaeicola algicola	78.1894	406	1088	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310325.1	s__Jejuia sp004310325	78.0551	342	1088	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:17:42,546] [INFO] GTDB search result was written to GCF_021728415.1_ASM2172841v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:17:42,547] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:17:42,550] [INFO] DFAST_QC result json was written to GCF_021728415.1_ASM2172841v1_genomic.fna/dqc_result.json
[2024-01-25 18:17:42,550] [INFO] DFAST_QC completed!
[2024-01-25 18:17:42,550] [INFO] Total running time: 0h1m7s