[2024-01-25 18:58:05,717] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:58:05,718] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:58:05,718] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ca9eb80-2070-480b-b10d-222592c6991d/dqc_reference
[2024-01-25 18:58:06,875] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:58:06,876] [INFO] Task started: Prodigal
[2024-01-25 18:58:06,876] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe6b4454-490e-4d9b-9fa8-417661df1fd4/GCF_001310225.1_ASM131022v1_genomic.fna.gz | prodigal -d GCF_001310225.1_ASM131022v1_genomic.fna/cds.fna -a GCF_001310225.1_ASM131022v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:58:17,461] [INFO] Task succeeded: Prodigal
[2024-01-25 18:58:17,461] [INFO] Task started: HMMsearch
[2024-01-25 18:58:17,461] [INFO] Running command: hmmsearch --tblout GCF_001310225.1_ASM131022v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ca9eb80-2070-480b-b10d-222592c6991d/dqc_reference/reference_markers.hmm GCF_001310225.1_ASM131022v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:58:17,699] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:58:17,700] [INFO] Found 6/6 markers.
[2024-01-25 18:58:17,735] [INFO] Query marker FASTA was written to GCF_001310225.1_ASM131022v1_genomic.fna/markers.fasta
[2024-01-25 18:58:17,735] [INFO] Task started: Blastn
[2024-01-25 18:58:17,735] [INFO] Running command: blastn -query GCF_001310225.1_ASM131022v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ca9eb80-2070-480b-b10d-222592c6991d/dqc_reference/reference_markers.fasta -out GCF_001310225.1_ASM131022v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:18,402] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:18,406] [INFO] Selected 22 target genomes.
[2024-01-25 18:58:18,406] [INFO] Target genome list was writen to GCF_001310225.1_ASM131022v1_genomic.fna/target_genomes.txt
[2024-01-25 18:58:18,430] [INFO] Task started: fastANI
[2024-01-25 18:58:18,430] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe6b4454-490e-4d9b-9fa8-417661df1fd4/GCF_001310225.1_ASM131022v1_genomic.fna.gz --refList GCF_001310225.1_ASM131022v1_genomic.fna/target_genomes.txt --output GCF_001310225.1_ASM131022v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:58:34,260] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:34,261] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ca9eb80-2070-480b-b10d-222592c6991d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:58:34,261] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ca9eb80-2070-480b-b10d-222592c6991d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:58:34,274] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:58:34,274] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:58:34,274] [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
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	100.0	1331	1331	95	conclusive
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	78.6529	423	1331	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	78.5605	404	1331	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	78.5029	400	1331	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	78.4946	398	1331	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	78.4231	520	1331	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	78.407	439	1331	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	78.3998	440	1331	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	78.3402	437	1331	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	78.2999	381	1331	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	78.2015	386	1331	95	below_threshold
Confluentibacter lentus	strain=HJM-3	GCA_002806995.1	1699412	1699412	type	True	78.108	315	1331	95	below_threshold
Confluentibacter flavum	strain=3B	GCA_002843175.1	1909700	1909700	type	True	78.0803	347	1331	95	below_threshold
Confluentibacter sediminis	strain=DSL-48	GCA_003258355.1	2219045	2219045	type	True	78.0775	379	1331	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	77.9623	371	1331	95	below_threshold
Yeosuana marina	strain=JLT21	GCA_011762485.1	1565536	1565536	type	True	77.9213	384	1331	95	below_threshold
Yeosuana aromativorans	strain=JCM 12862	GCA_014646655.1	288019	288019	type	True	77.7355	276	1331	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	77.6988	238	1331	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.6965	207	1331	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	77.6934	374	1331	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.5257	235	1331	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.512	283	1331	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:58:34,310] [INFO] DFAST Taxonomy check result was written to GCF_001310225.1_ASM131022v1_genomic.fna/tc_result.tsv
[2024-01-25 18:58:34,310] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:58:34,310] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:58:34,311] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ca9eb80-2070-480b-b10d-222592c6991d/dqc_reference/checkm_data
[2024-01-25 18:58:34,312] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:58:34,354] [INFO] Task started: CheckM
[2024-01-25 18:58:34,354] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001310225.1_ASM131022v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001310225.1_ASM131022v1_genomic.fna/checkm_input GCF_001310225.1_ASM131022v1_genomic.fna/checkm_result
[2024-01-25 18:59:07,957] [INFO] Task succeeded: CheckM
[2024-01-25 18:59:07,959] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:59:07,997] [INFO] ===== Completeness check finished =====
[2024-01-25 18:59:07,997] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:59:07,997] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001310225.1_ASM131022v1_genomic.fna/markers.fasta)
[2024-01-25 18:59:07,998] [INFO] Task started: Blastn
[2024-01-25 18:59:07,998] [INFO] Running command: blastn -query GCF_001310225.1_ASM131022v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ca9eb80-2070-480b-b10d-222592c6991d/dqc_reference/reference_markers_gtdb.fasta -out GCF_001310225.1_ASM131022v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:09,009] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:09,012] [INFO] Selected 20 target genomes.
[2024-01-25 18:59:09,012] [INFO] Target genome list was writen to GCF_001310225.1_ASM131022v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:59:09,050] [INFO] Task started: fastANI
[2024-01-25 18:59:09,050] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe6b4454-490e-4d9b-9fa8-417661df1fd4/GCF_001310225.1_ASM131022v1_genomic.fna.gz --refList GCF_001310225.1_ASM131022v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001310225.1_ASM131022v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:59:24,443] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:24,455] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:59:24,455] [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_001310225.1	s__Algibacter_A alginicilyticus	100.0	1330	1331	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900114265.1	s__Flaviramulus basaltis	78.9187	467	1331	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789235.1	s__Wocania ichthyoenteri	78.7327	442	1331	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	78.6527	422	1331	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_900141715.1	s__Arenitalea lutea	78.5133	399	1331	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004341235.1	s__Mariniflexile fucanivorans	78.4242	520	1331	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000941055.1	s__Siansivirga zeaxanthinifaciens	78.3778	362	1331	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Siansivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971785.1	s__Seonamhaeicola sp001971785	78.3708	414	1331	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747085.1	s__Algibacter_C aquaticus	78.3591	438	1331	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_014202225.1	s__Algibacter_B amylolyticus	78.3534	437	1331	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_018860245.1	s__Tamlana_A agarivorans_A	78.322	337	1331	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_004791695.1	s__Flavivirga rizhaonensis	78.1892	387	1331	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002806995.1	s__Confluentibacter lentus	78.0863	318	1331	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741945.1	s__Wocania sp002741945	78.0711	427	1331	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002843175.1	s__Confluentibacter flavum	78.0683	345	1331	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003258355.1	s__Confluentibacter sp003258355	78.0503	382	1331	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997385.1	s__Seonamhaeicola algicola	77.9625	371	1331	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762485.1	s__Yeosuana marina	77.9348	385	1331	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610635.1	s__Ichthyenterobacterium magnum	77.927	272	1331	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ichthyenterobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002807055.1	s__Confluentibacter citreus	77.8904	330	1331	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:59:24,457] [INFO] GTDB search result was written to GCF_001310225.1_ASM131022v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:59:24,457] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:59:24,461] [INFO] DFAST_QC result json was written to GCF_001310225.1_ASM131022v1_genomic.fna/dqc_result.json
[2024-01-25 18:59:24,462] [INFO] DFAST_QC completed!
[2024-01-25 18:59:24,462] [INFO] Total running time: 0h1m19s