[2024-01-25 18:06:05,617] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:06:05,618] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:06:05,618] [INFO] DQC Reference Directory: /var/lib/cwl/stg06140fec-ddd6-48b8-8796-41c91016afb1/dqc_reference
[2024-01-25 18:06:06,790] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:06:06,791] [INFO] Task started: Prodigal
[2024-01-25 18:06:06,791] [INFO] Running command: gunzip -c /var/lib/cwl/stgb2feea35-6e82-45bc-88b5-7929221a016f/GCF_003148645.1_ASM314864v1_genomic.fna.gz | prodigal -d GCF_003148645.1_ASM314864v1_genomic.fna/cds.fna -a GCF_003148645.1_ASM314864v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:06:14,550] [INFO] Task succeeded: Prodigal
[2024-01-25 18:06:14,550] [INFO] Task started: HMMsearch
[2024-01-25 18:06:14,550] [INFO] Running command: hmmsearch --tblout GCF_003148645.1_ASM314864v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06140fec-ddd6-48b8-8796-41c91016afb1/dqc_reference/reference_markers.hmm GCF_003148645.1_ASM314864v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:06:14,752] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:06:14,753] [INFO] Found 6/6 markers.
[2024-01-25 18:06:14,779] [INFO] Query marker FASTA was written to GCF_003148645.1_ASM314864v1_genomic.fna/markers.fasta
[2024-01-25 18:06:14,779] [INFO] Task started: Blastn
[2024-01-25 18:06:14,779] [INFO] Running command: blastn -query GCF_003148645.1_ASM314864v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06140fec-ddd6-48b8-8796-41c91016afb1/dqc_reference/reference_markers.fasta -out GCF_003148645.1_ASM314864v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:15,432] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:15,435] [INFO] Selected 23 target genomes.
[2024-01-25 18:06:15,436] [INFO] Target genome list was writen to GCF_003148645.1_ASM314864v1_genomic.fna/target_genomes.txt
[2024-01-25 18:06:15,460] [INFO] Task started: fastANI
[2024-01-25 18:06:15,460] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2feea35-6e82-45bc-88b5-7929221a016f/GCF_003148645.1_ASM314864v1_genomic.fna.gz --refList GCF_003148645.1_ASM314864v1_genomic.fna/target_genomes.txt --output GCF_003148645.1_ASM314864v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:06:31,001] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:31,001] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06140fec-ddd6-48b8-8796-41c91016afb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:06:31,001] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06140fec-ddd6-48b8-8796-41c91016afb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:06:31,014] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:06:31,014] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:06:31,014] [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
Xanthomarina gelatinilytica	strain=AK20	GCA_000348685.1	1137281	1137281	type	True	80.5744	623	1037	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	78.508	426	1037	95	below_threshold
Oceanihabitans sediminis	strain=DSM 28133	GCA_003315315.1	1812012	1812012	type	True	78.4475	329	1037	95	below_threshold
Oceanihabitans sediminis	strain=S9-10	GCA_003337215.1	1812012	1812012	type	True	78.4077	329	1037	95	below_threshold
Bizionia echini	strain=DSM 23925	GCA_900115185.1	649333	649333	type	True	78.3749	390	1037	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	78.3235	405	1037	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	78.1135	347	1037	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	78.0272	285	1037	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	78.0212	291	1037	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	78.0093	292	1037	95	below_threshold
Bizionia argentinensis	strain=JUB59	GCA_000224335.2	456455	456455	type	True	77.9813	320	1037	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	77.9132	282	1037	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	77.8954	242	1037	95	below_threshold
Flavivirga eckloniae	strain=ECD14	GCA_002886045.1	1803846	1803846	type	True	77.8895	257	1037	95	below_threshold
Formosa haliotis	strain=LMG 28520	GCA_001685485.1	1555194	1555194	type	True	77.8786	284	1037	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.873	261	1037	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	77.8572	298	1037	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.8352	308	1037	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	77.7655	307	1037	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	77.7416	286	1037	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	77.7213	285	1037	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	77.4699	248	1037	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.0272	210	1037	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:06:31,016] [INFO] DFAST Taxonomy check result was written to GCF_003148645.1_ASM314864v1_genomic.fna/tc_result.tsv
[2024-01-25 18:06:31,017] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:06:31,017] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:06:31,017] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06140fec-ddd6-48b8-8796-41c91016afb1/dqc_reference/checkm_data
[2024-01-25 18:06:31,018] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:06:31,051] [INFO] Task started: CheckM
[2024-01-25 18:06:31,051] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003148645.1_ASM314864v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003148645.1_ASM314864v1_genomic.fna/checkm_input GCF_003148645.1_ASM314864v1_genomic.fna/checkm_result
[2024-01-25 18:06:57,396] [INFO] Task succeeded: CheckM
[2024-01-25 18:06:57,397] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:06:57,414] [INFO] ===== Completeness check finished =====
[2024-01-25 18:06:57,414] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:06:57,415] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003148645.1_ASM314864v1_genomic.fna/markers.fasta)
[2024-01-25 18:06:57,415] [INFO] Task started: Blastn
[2024-01-25 18:06:57,415] [INFO] Running command: blastn -query GCF_003148645.1_ASM314864v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06140fec-ddd6-48b8-8796-41c91016afb1/dqc_reference/reference_markers_gtdb.fasta -out GCF_003148645.1_ASM314864v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:58,372] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:58,375] [INFO] Selected 7 target genomes.
[2024-01-25 18:06:58,375] [INFO] Target genome list was writen to GCF_003148645.1_ASM314864v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:06:58,380] [INFO] Task started: fastANI
[2024-01-25 18:06:58,380] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2feea35-6e82-45bc-88b5-7929221a016f/GCF_003148645.1_ASM314864v1_genomic.fna.gz --refList GCF_003148645.1_ASM314864v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003148645.1_ASM314864v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:07:03,651] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:03,656] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:07:03,656] [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_003148645.1	s__Xanthomarina spongicola	100.0	1035	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008084905.1	s__Xanthomarina maritima	84.1956	769	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002366675.1	s__Xanthomarina sp002366675	84.1619	544	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003144015.1	s__Xanthomarina sp003144015	83.5965	755	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638915.1	s__Xanthomarina arctica	81.1202	684	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000348685.1	s__Xanthomarina gelatinilytica	80.5674	623	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	98.37	98.31	0.90	0.88	4	-
GCF_012931685.1	s__Pseudobizionia ponticola	78.3808	387	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pseudobizionia	95.0	97.35	97.35	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:07:03,658] [INFO] GTDB search result was written to GCF_003148645.1_ASM314864v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:07:03,658] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:07:03,661] [INFO] DFAST_QC result json was written to GCF_003148645.1_ASM314864v1_genomic.fna/dqc_result.json
[2024-01-25 18:07:03,661] [INFO] DFAST_QC completed!
[2024-01-25 18:07:03,661] [INFO] Total running time: 0h0m58s