[2023-06-27 05:00:36,117] [INFO] DFAST_QC pipeline started.
[2023-06-27 05:00:36,121] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 05:00:36,121] [INFO] DQC Reference Directory: /var/lib/cwl/stg3af057eb-7d48-425e-aefb-f572e7dad0db/dqc_reference
[2023-06-27 05:00:37,397] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 05:00:37,398] [INFO] Task started: Prodigal
[2023-06-27 05:00:37,399] [INFO] Running command: gunzip -c /var/lib/cwl/stg0478493b-6eac-46ea-891f-37e5ce274844/GCA_002441545.1_ASM244154v1_genomic.fna.gz | prodigal -d GCA_002441545.1_ASM244154v1_genomic.fna/cds.fna -a GCA_002441545.1_ASM244154v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 05:00:48,484] [INFO] Task succeeded: Prodigal
[2023-06-27 05:00:48,484] [INFO] Task started: HMMsearch
[2023-06-27 05:00:48,485] [INFO] Running command: hmmsearch --tblout GCA_002441545.1_ASM244154v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3af057eb-7d48-425e-aefb-f572e7dad0db/dqc_reference/reference_markers.hmm GCA_002441545.1_ASM244154v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 05:00:48,754] [INFO] Task succeeded: HMMsearch
[2023-06-27 05:00:48,755] [INFO] Found 6/6 markers.
[2023-06-27 05:00:48,793] [INFO] Query marker FASTA was written to GCA_002441545.1_ASM244154v1_genomic.fna/markers.fasta
[2023-06-27 05:00:48,793] [INFO] Task started: Blastn
[2023-06-27 05:00:48,793] [INFO] Running command: blastn -query GCA_002441545.1_ASM244154v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3af057eb-7d48-425e-aefb-f572e7dad0db/dqc_reference/reference_markers.fasta -out GCA_002441545.1_ASM244154v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:00:49,469] [INFO] Task succeeded: Blastn
[2023-06-27 05:00:49,477] [INFO] Selected 24 target genomes.
[2023-06-27 05:00:49,478] [INFO] Target genome list was writen to GCA_002441545.1_ASM244154v1_genomic.fna/target_genomes.txt
[2023-06-27 05:00:49,491] [INFO] Task started: fastANI
[2023-06-27 05:00:49,491] [INFO] Running command: fastANI --query /var/lib/cwl/stg0478493b-6eac-46ea-891f-37e5ce274844/GCA_002441545.1_ASM244154v1_genomic.fna.gz --refList GCA_002441545.1_ASM244154v1_genomic.fna/target_genomes.txt --output GCA_002441545.1_ASM244154v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 05:01:05,331] [INFO] Task succeeded: fastANI
[2023-06-27 05:01:05,331] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3af057eb-7d48-425e-aefb-f572e7dad0db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 05:01:05,332] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3af057eb-7d48-425e-aefb-f572e7dad0db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 05:01:05,356] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 05:01:05,357] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 05:01:05,357] [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
Yeosuana marina	strain=JLT21	GCA_011762485.1	1565536	1565536	type	True	79.7666	577	1106	95	below_threshold
Yeosuana aromativorans	strain=JCM 12862	GCA_014646655.1	288019	288019	type	True	79.3075	461	1106	95	below_threshold
Confluentibacter flavum	strain=3B	GCA_002843175.1	1909700	1909700	type	True	78.4181	359	1106	95	below_threshold
Confluentibacter sediminis	strain=DSL-48	GCA_003258355.1	2219045	2219045	type	True	78.3864	370	1106	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	78.3627	376	1106	95	below_threshold
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	78.0281	350	1106	95	below_threshold
Confluentibacter lentus	strain=HJM-3	GCA_002806995.1	1699412	1699412	type	True	77.9856	331	1106	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	77.9007	349	1106	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	77.8224	341	1106	95	below_threshold
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	77.7546	306	1106	95	below_threshold
Changchengzhania lutea	strain=SM1355	GCA_006974145.1	2049305	2049305	type	True	77.6952	277	1106	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.6758	291	1106	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	77.5609	309	1106	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	77.5108	315	1106	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	77.4814	296	1106	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.3708	256	1106	95	below_threshold
Snuella sedimenti	strain=CAU 1569	GCA_016428595.1	2798802	2798802	type	True	77.2914	236	1106	95	below_threshold
Oceanihabitans sediminis	strain=S9-10	GCA_003337215.1	1812012	1812012	type	True	77.2097	203	1106	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.1106	219	1106	95	below_threshold
Tamlana haliotis	strain=B1N29	GCA_008806375.1	2614804	2614804	type	True	77.0528	210	1106	95	below_threshold
Olleya marilimosa	strain=CAM030	GCA_000518485.1	272164	272164	type	True	77.0214	204	1106	95	below_threshold
Xanthomarina gelatinilytica	strain=AK20	GCA_000348685.1	1137281	1137281	type	True	76.9578	179	1106	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.8962	208	1106	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.8867	158	1106	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 05:01:05,367] [INFO] DFAST Taxonomy check result was written to GCA_002441545.1_ASM244154v1_genomic.fna/tc_result.tsv
[2023-06-27 05:01:05,368] [INFO] ===== Taxonomy check completed =====
[2023-06-27 05:01:05,368] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 05:01:05,369] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3af057eb-7d48-425e-aefb-f572e7dad0db/dqc_reference/checkm_data
[2023-06-27 05:01:05,370] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 05:01:05,415] [INFO] Task started: CheckM
[2023-06-27 05:01:05,415] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002441545.1_ASM244154v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002441545.1_ASM244154v1_genomic.fna/checkm_input GCA_002441545.1_ASM244154v1_genomic.fna/checkm_result
[2023-06-27 05:01:41,256] [INFO] Task succeeded: CheckM
[2023-06-27 05:01:41,258] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.40%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-27 05:01:41,278] [INFO] ===== Completeness check finished =====
[2023-06-27 05:01:41,279] [INFO] ===== Start GTDB Search =====
[2023-06-27 05:01:41,279] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002441545.1_ASM244154v1_genomic.fna/markers.fasta)
[2023-06-27 05:01:41,279] [INFO] Task started: Blastn
[2023-06-27 05:01:41,280] [INFO] Running command: blastn -query GCA_002441545.1_ASM244154v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3af057eb-7d48-425e-aefb-f572e7dad0db/dqc_reference/reference_markers_gtdb.fasta -out GCA_002441545.1_ASM244154v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:01:42,161] [INFO] Task succeeded: Blastn
[2023-06-27 05:01:42,166] [INFO] Selected 16 target genomes.
[2023-06-27 05:01:42,166] [INFO] Target genome list was writen to GCA_002441545.1_ASM244154v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 05:01:42,172] [INFO] Task started: fastANI
[2023-06-27 05:01:42,172] [INFO] Running command: fastANI --query /var/lib/cwl/stg0478493b-6eac-46ea-891f-37e5ce274844/GCA_002441545.1_ASM244154v1_genomic.fna.gz --refList GCA_002441545.1_ASM244154v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002441545.1_ASM244154v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 05:01:52,711] [INFO] Task succeeded: fastANI
[2023-06-27 05:01:52,726] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 05:01:52,726] [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_002441545.1	s__Yeosuana sp002441545	100.0	1100	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002784145.1	s__Yeosuana sp002784145	80.4869	507	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	99.75	99.57	0.88	0.85	11	-
GCF_011762485.1	s__Yeosuana marina	79.7615	578	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646655.1	s__Yeosuana aromativorans	79.3075	461	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	78.5195	430	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002843175.1	s__Confluentibacter flavum	78.4181	359	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789235.1	s__Wocania ichthyoenteri	78.1327	363	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017814435.1	s__Mariniflexile gromovii	78.0186	351	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791695.1	s__Flavivirga rizhaonensis	77.8944	349	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001310225.1	s__Algibacter_A alginicilyticus	77.7469	306	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971785.1	s__Seonamhaeicola sp001971785	77.6527	333	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148645.1	s__Xanthomarina spongicola	77.6078	263	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641635.1	s__Aquaticitalea lipolytica	77.465	290	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610635.1	s__Ichthyenterobacterium magnum	77.4361	235	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ichthyenterobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638915.1	s__Xanthomarina arctica	77.2819	231	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162765.1	s__MAAR01 sp002162765	77.1646	167	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAAR01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 05:01:52,729] [INFO] GTDB search result was written to GCA_002441545.1_ASM244154v1_genomic.fna/result_gtdb.tsv
[2023-06-27 05:01:52,729] [INFO] ===== GTDB Search completed =====
[2023-06-27 05:01:52,734] [INFO] DFAST_QC result json was written to GCA_002441545.1_ASM244154v1_genomic.fna/dqc_result.json
[2023-06-27 05:01:52,734] [INFO] DFAST_QC completed!
[2023-06-27 05:01:52,734] [INFO] Total running time: 0h1m17s