[2024-01-25 18:09:35,522] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:09:35,524] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:09:35,524] [INFO] DQC Reference Directory: /var/lib/cwl/stg39062c57-e90b-4d78-99b6-a86863f1e28a/dqc_reference
[2024-01-25 18:09:36,674] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:09:36,675] [INFO] Task started: Prodigal
[2024-01-25 18:09:36,675] [INFO] Running command: gunzip -c /var/lib/cwl/stg879009d6-1316-4e0e-869a-34c9986498a8/GCF_030540875.1_ASM3054087v1_genomic.fna.gz | prodigal -d GCF_030540875.1_ASM3054087v1_genomic.fna/cds.fna -a GCF_030540875.1_ASM3054087v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:09:48,858] [INFO] Task succeeded: Prodigal
[2024-01-25 18:09:48,858] [INFO] Task started: HMMsearch
[2024-01-25 18:09:48,858] [INFO] Running command: hmmsearch --tblout GCF_030540875.1_ASM3054087v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39062c57-e90b-4d78-99b6-a86863f1e28a/dqc_reference/reference_markers.hmm GCF_030540875.1_ASM3054087v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:09:49,161] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:09:49,164] [INFO] Found 6/6 markers.
[2024-01-25 18:09:49,202] [INFO] Query marker FASTA was written to GCF_030540875.1_ASM3054087v1_genomic.fna/markers.fasta
[2024-01-25 18:09:49,202] [INFO] Task started: Blastn
[2024-01-25 18:09:49,202] [INFO] Running command: blastn -query GCF_030540875.1_ASM3054087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39062c57-e90b-4d78-99b6-a86863f1e28a/dqc_reference/reference_markers.fasta -out GCF_030540875.1_ASM3054087v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:49,874] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:49,877] [INFO] Selected 15 target genomes.
[2024-01-25 18:09:49,877] [INFO] Target genome list was writen to GCF_030540875.1_ASM3054087v1_genomic.fna/target_genomes.txt
[2024-01-25 18:09:49,879] [INFO] Task started: fastANI
[2024-01-25 18:09:49,879] [INFO] Running command: fastANI --query /var/lib/cwl/stg879009d6-1316-4e0e-869a-34c9986498a8/GCF_030540875.1_ASM3054087v1_genomic.fna.gz --refList GCF_030540875.1_ASM3054087v1_genomic.fna/target_genomes.txt --output GCF_030540875.1_ASM3054087v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:10:00,950] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:00,950] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39062c57-e90b-4d78-99b6-a86863f1e28a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:10:00,951] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39062c57-e90b-4d78-99b6-a86863f1e28a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:10:00,960] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:10:00,960] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:10:00,961] [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
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	87.1395	1035	1612	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	82.3457	880	1612	95	below_threshold
Flavivirga eckloniae	strain=ECD14	GCA_002886045.1	1803846	1803846	type	True	81.2966	917	1612	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	78.9542	533	1612	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	78.6991	419	1612	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	78.5424	468	1612	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	78.4778	473	1612	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	78.3736	456	1612	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	78.3589	461	1612	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	78.3181	466	1612	95	below_threshold
Tamlana haliotis	strain=B1N29	GCA_008806375.1	2614804	2614804	type	True	78.0258	359	1612	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.996	382	1612	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.5269	256	1612	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.5144	335	1612	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.2178	258	1612	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:10:00,962] [INFO] DFAST Taxonomy check result was written to GCF_030540875.1_ASM3054087v1_genomic.fna/tc_result.tsv
[2024-01-25 18:10:00,963] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:10:00,963] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:10:00,963] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39062c57-e90b-4d78-99b6-a86863f1e28a/dqc_reference/checkm_data
[2024-01-25 18:10:00,964] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:10:01,010] [INFO] Task started: CheckM
[2024-01-25 18:10:01,010] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030540875.1_ASM3054087v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030540875.1_ASM3054087v1_genomic.fna/checkm_input GCF_030540875.1_ASM3054087v1_genomic.fna/checkm_result
[2024-01-25 18:10:37,926] [INFO] Task succeeded: CheckM
[2024-01-25 18:10:37,928] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:10:37,950] [INFO] ===== Completeness check finished =====
[2024-01-25 18:10:37,950] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:10:37,951] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030540875.1_ASM3054087v1_genomic.fna/markers.fasta)
[2024-01-25 18:10:37,951] [INFO] Task started: Blastn
[2024-01-25 18:10:37,951] [INFO] Running command: blastn -query GCF_030540875.1_ASM3054087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39062c57-e90b-4d78-99b6-a86863f1e28a/dqc_reference/reference_markers_gtdb.fasta -out GCF_030540875.1_ASM3054087v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:38,923] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:38,926] [INFO] Selected 10 target genomes.
[2024-01-25 18:10:38,926] [INFO] Target genome list was writen to GCF_030540875.1_ASM3054087v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:10:38,936] [INFO] Task started: fastANI
[2024-01-25 18:10:38,936] [INFO] Running command: fastANI --query /var/lib/cwl/stg879009d6-1316-4e0e-869a-34c9986498a8/GCF_030540875.1_ASM3054087v1_genomic.fna.gz --refList GCF_030540875.1_ASM3054087v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030540875.1_ASM3054087v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:10:47,866] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:47,873] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:10:47,873] [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_004791695.1	s__Flavivirga rizhaonensis	87.1546	1034	1612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910715.1	s__Flavivirga sp012910715	82.3396	881	1612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002886045.1	s__Flavivirga eckloniae	81.3098	915	1612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	79.5184	552	1612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747085.1	s__Algibacter_C aquaticus	79.2162	633	1612	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_000789235.1	s__Wocania ichthyoenteri	79.03	536	1612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	78.9575	533	1612	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_014202225.1	s__Algibacter_B amylolyticus	78.5429	469	1612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	100.00	100.00	1.00	1.00	3	-
GCF_900141715.1	s__Arenitalea lutea	78.3316	465	1612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008806375.1	s__Tamlana_A haliotis	78.0249	359	1612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:10:47,875] [INFO] GTDB search result was written to GCF_030540875.1_ASM3054087v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:10:47,875] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:10:47,878] [INFO] DFAST_QC result json was written to GCF_030540875.1_ASM3054087v1_genomic.fna/dqc_result.json
[2024-01-25 18:10:47,878] [INFO] DFAST_QC completed!
[2024-01-25 18:10:47,878] [INFO] Total running time: 0h1m12s